sam, hierarchical clustering (treeview) Search Results


treeview  (SourceForge net)
90
SourceForge net treeview
Treeview, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/treeview/pmc04888481-378-7-9
Average 90 stars, based on 1 article reviews
treeview - by Bioz Stars, 2026-11
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cluster and treeview  (SourceForge net)
90
SourceForge net cluster and treeview
Cluster And Treeview, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/treeview+software/pmc06521571-61-17-19
Average 90 stars, based on 1 article reviews
cluster and treeview - by Bioz Stars, 2026-11
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treeview v1.16r4  (SourceForge net)
90
SourceForge net treeview v1.16r4
KEY RESOURCES TABLE
Treeview V1.16r4, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/treeview+v1+16r4/pmc06128737-124-0-6
Average 90 stars, based on 1 article reviews
treeview v1.16r4 - by Bioz Stars, 2026-11
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treeview v3  (SourceForge net)
90
SourceForge net treeview v3
KEY RESOURCES TABLE
Treeview V3, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/treeview+v3/pmc04760761-252-26-29
Average 90 stars, based on 1 article reviews
treeview v3 - by Bioz Stars, 2026-11
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treeview 1.1  (Broad Institute Inc)
90
Broad Institute Inc treeview 1.1
KEY RESOURCES TABLE
Treeview 1.1, supplied by Broad Institute 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/sam%2C+hierarchical+clustering+(treeview)/treeview+1+1/pmc05762420-609-4-8
Average 90 stars, based on 1 article reviews
treeview 1.1 - by Bioz Stars, 2026-11
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snomad  (Johns Hopkins HealthCare)
90
Johns Hopkins HealthCare snomad
Some of the available informatic tools that can be applied towards OMIC analyses
Snomad, supplied by Johns Hopkins HealthCare, 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/sam%2C+hierarchical+clustering+(treeview)/snomad/pmc02993238-212-28-26
Average 90 stars, based on 1 article reviews
snomad - by Bioz Stars, 2026-11
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treeview 1.0.13  (SourceForge net)
90
SourceForge net treeview 1.0.13
Some of the available informatic tools that can be applied towards OMIC analyses
Treeview 1.0.13, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/treeview+1+0+13/pm17485540-75-6-8
Average 90 stars, based on 1 article reviews
treeview 1.0.13 - by Bioz Stars, 2026-11
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treeview (cluster 3.0)  (SourceForge net)
90
SourceForge net treeview (cluster 3.0)
a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
Treeview (Cluster 3.0), supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/cluster+3+0/pmc10362017-30-13-18
Average 90 stars, based on 1 article reviews
treeview (cluster 3.0) - by Bioz Stars, 2026-11
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picardtools version 1.96  (SourceForge net)
90
SourceForge net picardtools version 1.96
a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
Picardtools Version 1.96, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/picardtools+version+1+96/pmc10539308__41467_2023_41793_MOESM3_ESM-11-35-42
Average 90 stars, based on 1 article reviews
picardtools version 1.96 - by Bioz Stars, 2026-11
90/100 stars
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image generation program treeview  (SourceForge net)
90
SourceForge net image generation program treeview
a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
Image Generation Program Treeview, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/image+generation+program+treeview/pm36220877-138-24-29
Average 90 stars, based on 1 article reviews
image generation program treeview - by Bioz Stars, 2026-11
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java treeview  (SourceForge net)
90
SourceForge net java treeview
a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
Java Treeview, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/java+treeview/pm15153179-192-7-13
Average 90 stars, based on 1 article reviews
java treeview - by Bioz Stars, 2026-11
90/100 stars
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treeview (version 1.1.6r4  (SourceForge net)
90
SourceForge net treeview (version 1.1.6r4
a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using <t>TreeView</t> (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.
Treeview (Version 1.1.6r4, supplied by SourceForge net, 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/sam%2C+hierarchical+clustering+(treeview)/java+treeview+1+1+3/pmc07475442-164-8-13
Average 90 stars, based on 1 article reviews
treeview (version 1.1.6r4 - by Bioz Stars, 2026-11
90/100 stars
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Image Search Results


KEY RESOURCES TABLE

Journal: Cell stem cell

Article Title: Dppa2/4 facilitate epigenetic remodeling during reprogramming to pluripotency

doi: 10.1016/j.stem.2018.08.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: TreeView v1.16r4 , (Saldanha, 2004) , https://sourceforge.net/projects/jtreeview/files/.

Techniques: Cell Analysis, Recombinant, SYBR Green Assay, Staining, Reverse Transcription, Protease Inhibitor, Magnetic Beads, RNA Amplification, Purification, Silver Staining, Isolation, Mouse Assay, Software

Some of the available informatic tools that can be applied towards OMIC analyses

Journal:

Article Title: De-Convoluting the "Omics" for Organ Transplantation

doi: 10.1097/MOT.0b013e32833068fb

Figure Lengend Snippet: Some of the available informatic tools that can be applied towards OMIC analyses

Article Snippet: Genomic Research) X-Miner (X-Mine) R: Statistics for Microarray Analysis (Terry Speed, UC Berkeley) Xpression NTI (InforMax) SAM: Significance Analysis of Microarrays (Tibshirani, Stanford) SNOMAD (Jonathan Pevsner, Johns Hopkins) TreeView (Michael Eisen, LBNL) XCluster (Gavin Sherlock, Stanford) Open in a separate window Some of the available informatic tools that can be applied towards OMIC analyses Data Warehousing and Reporting- essential requisites for collaborative data analysis Currently much of the data generated by an individual or group is still unavailable to the scientific community or in a format that is unusable by other laboratories.

Techniques: Microarray, Imaging, Expressing

a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.

Journal: Cell Death Discovery

Article Title: CAMK2D: a novel molecular target for BAP1 -deficient malignant mesothelioma

doi: 10.1038/s41420-023-01552-5

Figure Lengend Snippet: a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.

Article Snippet: The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ).

Techniques: CRISPR, Sequencing, Clone Assay, Expressing, Western Blot, Control, Gene Expression, Construct, Reverse Transcription Polymerase Chain Reaction