matlab umap package Search Results


image processing toolbox  (MathWorks Inc)
96
MathWorks Inc image processing toolbox
Image Processing Toolbox, supplied by MathWorks Inc, 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/result/image processing toolbox/product/MathWorks Inc
Average 96 stars, based on 1 article reviews
image processing toolbox - by Bioz Stars, 2026-06
96/100 stars
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rstudio 1.4.1106  (RStudio)
90
RStudio rstudio 1.4.1106
Rstudio 1.4.1106, supplied by RStudio, 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/result/rstudio 1.4.1106/product/RStudio
Average 90 stars, based on 1 article reviews
rstudio 1.4.1106 - by Bioz Stars, 2026-06
90/100 stars
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graphpad prism 6  (GraphPad Software Inc)
90
GraphPad Software Inc graphpad prism 6
Graphpad Prism 6, supplied by GraphPad Software 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/result/graphpad prism 6/product/GraphPad Software Inc
Average 90 stars, based on 1 article reviews
graphpad prism 6 - by Bioz Stars, 2026-06
90/100 stars
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rna seq data  (Addgene inc)
93
Addgene inc rna seq data
Rna Seq Data, supplied by Addgene inc, 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/result/rna seq data/product/Addgene inc
Average 93 stars, based on 1 article reviews
rna seq data - by Bioz Stars, 2026-06
93/100 stars
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zen blue 2.5  (Carl Zeiss)
90
Carl Zeiss zen blue 2.5
Zen Blue 2.5, supplied by Carl Zeiss, 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/result/zen blue 2.5/product/Carl Zeiss
Average 90 stars, based on 1 article reviews
zen blue 2.5 - by Bioz Stars, 2026-06
90/100 stars
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kanamycin vwr 408 levofloxacin sigmaaldrich 28266 meropenem sigmaaldrich 1392454 mitomycin sigmaaldrich y0000378 nigericin sigmaaldrich n7143  (Fisher Scientific)
86
Fisher Scientific kanamycin vwr 408 levofloxacin sigmaaldrich 28266 meropenem sigmaaldrich 1392454 mitomycin sigmaaldrich y0000378 nigericin sigmaaldrich n7143
Kanamycin Vwr 408 Levofloxacin Sigmaaldrich 28266 Meropenem Sigmaaldrich 1392454 Mitomycin Sigmaaldrich Y0000378 Nigericin Sigmaaldrich N7143, supplied by Fisher Scientific, 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/result/kanamycin vwr 408 levofloxacin sigmaaldrich 28266 meropenem sigmaaldrich 1392454 mitomycin sigmaaldrich y0000378 nigericin sigmaaldrich n7143/product/Fisher Scientific
Average 86 stars, based on 1 article reviews
kanamycin vwr 408 levofloxacin sigmaaldrich 28266 meropenem sigmaaldrich 1392454 mitomycin sigmaaldrich y0000378 nigericin sigmaaldrich n7143 - by Bioz Stars, 2026-06
86/100 stars
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nextflow (20.10.0  (SeqEra Labs)
90
SeqEra Labs nextflow (20.10.0
KEY RESOURCES TABLE
Nextflow (20.10.0, 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/result/nextflow (20.10.0/product/SeqEra Labs
Average 90 stars, based on 1 article reviews
nextflow (20.10.0 - by Bioz Stars, 2026-06
90/100 stars
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prism 8.2.1  (GraphPad Software Inc)
90
GraphPad Software Inc prism 8.2.1
KEY RESOURCES TABLE
Prism 8.2.1, supplied by GraphPad Software 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/result/prism 8.2.1/product/GraphPad Software Inc
Average 90 stars, based on 1 article reviews
prism 8.2.1 - by Bioz Stars, 2026-06
90/100 stars
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saline homemade n a phosphate  (Thermo Fisher)
99
Thermo Fisher saline homemade n a phosphate
KEY RESOURCES TABLE
Saline Homemade N A Phosphate, supplied by Thermo Fisher, 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/result/saline homemade n a phosphate/product/Thermo Fisher
Average 99 stars, based on 1 article reviews
saline homemade n a phosphate - by Bioz Stars, 2026-06
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Image Search Results


KEY RESOURCES TABLE

Journal: Cell reports

Article Title: AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells

doi: 10.1016/j.celrep.2022.111147

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: This paper N/A Software and algorithms Source code for analyses This paper https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma CellProfiler (3.1.9) ( McQuin et al., 2018 ) https://cellprofiler.org/ ImageJ (2.3.0) Public Domain Software https://imagej.nih.gov/ij/index.html MATLAB (2020b) Mathworks https://matlab.mathworks.com/ R (4.0.4) The Comprehensive R Archive Network (CRAN) https://www.r-project.org/ stats R package (4.1.2) The R Project https://stat.ethz.ch/R-manual/R-devel/library/stats/html/00Index.html AUCell R package (1.16.0) (Aibaretal., 2017) https://bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html umap R package (0.2.7.0) CRAN https://cran.r-project.org/web/packages/umap/ SCopeLoomR R package (0.13.0) Aerts Lab https://github.com/aertslab/SCopeLoomR Python (3.9.2) N/A https://www.python.org/downloads/ Scanpy (1.7.1) ( Wolf et al., 2018 ) https://github. com/scverse/scanpy pySCENIC (0.11.0) ( Van de Sande et al., 2020 ) https://github.com/aertslab/SCENICprotocol Nextflow (20.10.0) Seqera Labs https://www.nextflow.io/ Scikit-learn Library (0.24.1) ( Pedregosa et al., 2018 ) https://scikit-learn.org/stable/ SHAP ( Lundberg and Lee, 2017 ) https://github.com/slundberg/shap Other 96-well plates Corning Cat# 3904 Differentiation signature gene sets ( Tsoi et al., 2018 ) N/A Proliferative and Invasive phenotype gene sets ( Hoek et al., 2006 ) http://www.jurmo.ch/work_97.php List of bZIP transcription factor genes ( Vinson et al., 2002 ) https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma List of transcription factor genes ( Van de Sande et al., 2020 ) https://raw.githubusercontent.com/aertslab/pySCENIC/master/resources/hs_hgnc_tfs.txt Nextflow pipeline adapted for running SCENIC iteratively ( Wouters et al., 2020 ) https://github.com/aertslab/singlecellRNA_melanoma_paper R scripts adapted for extracting and filtering regulons from multiple SCENIC runs ( Wouters et al., 2020 ) https://github.com/aertslab/singlecellRNA_melanoma_paper Homo sapiens whole-genome motif ranking databases for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/ Motif annotation file for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/ Open in a separate window KEY RESOURCES TABLE The original codes for data analysis performed in this paper are publicly available at GitHub: https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma ( https://doi.org/10.5281/zenodo.6741989 ).

Techniques: Recombinant, Blocking Assay, Expressing, Activity Assay, Software

KEY RESOURCES TABLE

Journal: Cell reports

Article Title: AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells

doi: 10.1016/j.celrep.2022.111147

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: This paper N/A Software and algorithms Source code for analyses This paper https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma CellProfiler (3.1.9) ( McQuin et al., 2018 ) https://cellprofiler.org/ ImageJ (2.3.0) Public Domain Software https://imagej.nih.gov/ij/index.html MATLAB (2020b) Mathworks https://matlab.mathworks.com/ R (4.0.4) The Comprehensive R Archive Network (CRAN) https://www.r-project.org/ stats R package (4.1.2) The R Project https://stat.ethz.ch/R-manual/R-devel/library/stats/html/00Index.html AUCell R package (1.16.0) (Aibaretal., 2017) https://bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html umap R package (0.2.7.0) CRAN https://cran.r-project.org/web/packages/umap/ SCopeLoomR R package (0.13.0) Aerts Lab https://github.com/aertslab/SCopeLoomR Python (3.9.2) N/A https://www.python.org/downloads/ Scanpy (1.7.1) ( Wolf et al., 2018 ) https://github. com/scverse/scanpy pySCENIC (0.11.0) ( Van de Sande et al., 2020 ) https://github.com/aertslab/SCENICprotocol Nextflow (20.10.0) Seqera Labs https://www.nextflow.io/ Scikit-learn Library (0.24.1) ( Pedregosa et al., 2018 ) https://scikit-learn.org/stable/ SHAP ( Lundberg and Lee, 2017 ) https://github.com/slundberg/shap Other 96-well plates Corning Cat# 3904 Differentiation signature gene sets ( Tsoi et al., 2018 ) N/A Proliferative and Invasive phenotype gene sets ( Hoek et al., 2006 ) http://www.jurmo.ch/work_97.php List of bZIP transcription factor genes ( Vinson et al., 2002 ) https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma List of transcription factor genes ( Van de Sande et al., 2020 ) https://raw.githubusercontent.com/aertslab/pySCENIC/master/resources/hs_hgnc_tfs.txt Nextflow pipeline adapted for running SCENIC iteratively ( Wouters et al., 2020 ) https://github.com/aertslab/singlecellRNA_melanoma_paper R scripts adapted for extracting and filtering regulons from multiple SCENIC runs ( Wouters et al., 2020 ) https://github.com/aertslab/singlecellRNA_melanoma_paper Homo sapiens whole-genome motif ranking databases for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/ Motif annotation file for SCENIC (motif collection v9) Aerts Lab https://resources.aertslab.org/cistarget/ Open in a separate window KEY RESOURCES TABLE The original codes for data analysis performed in this paper are publicly available at GitHub: https://github.com/fallahi-sichani-lab/AP1-networkPlasticityMelanoma ( https://doi.org/10.5281/zenodo.6741989 ).

Techniques: Recombinant, Blocking Assay, Expressing, Activity Assay, Software