integrated rna-seq analysis pipeline irap 1.0.1 Search Results


nextflow v23.10.1 rna-seq pipeline  (SeqEra Labs)
90
SeqEra Labs nextflow v23.10.1 rna-seq pipeline
Nextflow V23.10.1 Rna Seq Pipeline, supplied by SeqEra Labs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/nextflow/pmc12108302-116-22-21
Average 90 stars, based on 1 article reviews
nextflow v23.10.1 rna-seq pipeline - by Bioz Stars, 2026-10
90/100 stars
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arraystudio rna-seq analysis pipeline  (OmicSoft Corporation)
90
OmicSoft Corporation arraystudio rna-seq analysis pipeline
Arraystudio Rna Seq Analysis Pipeline, supplied by OmicSoft Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/arraystudio+rna+seq+analysis+pipeline/pm36536241-519-7-6
Average 90 stars, based on 1 article reviews
arraystudio rna-seq analysis pipeline - by Bioz Stars, 2026-10
90/100 stars
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rna-seq process pipeline in omicsoft array studio software  (OmicSoft Corporation)
90
OmicSoft Corporation rna-seq process pipeline in omicsoft array studio software
Rna Seq Process Pipeline In Omicsoft Array Studio Software, supplied by OmicSoft Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/rna+seq+process+pipeline+in+omicsoft+array+studio+software/pm33979622-379-16-16
Average 90 stars, based on 1 article reviews
rna-seq process pipeline in omicsoft array studio software - by Bioz Stars, 2026-10
90/100 stars
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cell ranger arc 1 0 1 atac genome  (10X Genomics)
86
10X Genomics cell ranger arc 1 0 1 atac genome
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Cell Ranger Arc 1 0 1 Atac Genome, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/atac+cell+chromium+kit+library+single/pmc10076224-293-29-27
Average 86 stars, based on 1 article reviews
cell ranger arc 1 0 1 atac genome - by Bioz Stars, 2026-10
86/100 stars
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grch38 3 0 0 pre mrna human reference genome  (10X Genomics)
86
10X Genomics grch38 3 0 0 pre mrna human reference genome
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Grch38 3 0 0 Pre Mrna Human Reference Genome, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/cellranger/pmc10076224-293-20-18
Average 86 stars, based on 1 article reviews
grch38 3 0 0 pre mrna human reference genome - by Bioz Stars, 2026-10
86/100 stars
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c1 sequencing libraries  (fluidigm)
96
fluidigm c1 sequencing libraries
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
C1 Sequencing Libraries, supplied by fluidigm, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/C1/pmc06710272-344-70-63
Average 96 stars, based on 1 article reviews
c1 sequencing libraries - by Bioz Stars, 2026-10
96/100 stars
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novaseq 6000 s2 reagent kit v1 5  (Illumina Inc)
98
Illumina Inc novaseq 6000 s2 reagent kit v1 5
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Novaseq 6000 S2 Reagent Kit V1 5, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/NovaSeq+6000+S2+Reagent+Kit/pm39919738-189-91-99
Average 98 stars, based on 1 article reviews
novaseq 6000 s2 reagent kit v1 5 - by Bioz Stars, 2026-10
98/100 stars
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qupath v 0 5 1 qupath  (Bio-Rad)
99
Bio-Rad qupath v 0 5 1 qupath
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Qupath V 0 5 1 Qupath, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/Image+Lab+Software/pm39919738-189-216-224
Average 99 stars, based on 1 article reviews
qupath v 0 5 1 qupath - by Bioz Stars, 2026-10
99/100 stars
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stemdiff trilineage differentiation kit stemcell cat#05230  (STEMCELL Technologies Inc)
90
STEMCELL Technologies Inc stemdiff trilineage differentiation kit stemcell cat#05230
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Stemdiff Trilineage Differentiation Kit Stemcell Cat#05230, supplied by STEMCELL Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/stemdifftm+trilineage+differentiation+kit/pm39809262-180-59-63
Average 90 stars, based on 1 article reviews
stemdiff trilineage differentiation kit stemcell cat#05230 - by Bioz Stars, 2026-10
90/100 stars
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strand ngs software  (Strand Life Sciences Private)
90
Strand Life Sciences Private strand ngs software
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Strand Ngs Software, supplied by Strand Life Sciences Private, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/strand+ngs+software/pm35855895-133-84-89
Average 90 stars, based on 1 article reviews
strand ngs software - by Bioz Stars, 2026-10
90/100 stars
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cell lines human  (DSMZ)
93
DSMZ cell lines human
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Cell Lines Human, supplied by DSMZ, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/integrated+rna-seq+analysis+pipeline+irap+1%2E0%2E1/HCEC-B4G12/pm39809262-180-91-103
Average 93 stars, based on 1 article reviews
cell lines human - by Bioz Stars, 2026-10
93/100 stars
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facsdiva v.8.0.1  (Becton Dickinson)
90
Becton Dickinson facsdiva v.8.0.1
a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei <t>ATAC</t> sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).
Facsdiva V.8.0.1, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei ATAC sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).

Journal: Nature

Article Title: Spatial multiomics map of trophoblast development in early pregnancy

doi: 10.1038/s41586-023-05869-0

Figure Lengend Snippet: a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei ATAC sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).

Article Snippet: For each sequenced snRNA-seq and ATAC–seq (multiome) library, we performed read alignment to custom made genome consisting of 10X Genomics’ GRCh38 3.0.0 pre-mRNA human reference genome and 10X Genomics Cell Ranger-Arc 1.0.1 ATAC genome, created following instructions from 10X Genomics: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references .

Techniques: RNA Sequencing, Sequencing, RNA Expression