Recent changes to Packageshttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/Recent changes to PackagesenTue, 14 Feb 2023 13:08:08 -0000Packages modified by jakelinhttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v6 +++ v7 @@ -26,3 +26,9 @@ Enrichment visualizations |enrichplot| 1.4.0 Gene relevance based on multiple evidences in complex networks: https://www.itb.cnr.it/mnd [Snippets] + +PRS construction +PRS-CS |https://github.com/getian107/PRScs| infers posterior SNP effect sizes under continuous shrinkage (CS) priors using GWAS summary statistics and an external LD reference panel +PLINK2 + + </pre> </div>jakelinTue, 14 Feb 2023 13:08:08 -0000https://sourceforge.net6de87e36782ad229fb2c5defa0721d298da123a5Packages modified by Reija Autiohttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -5,25 +5,24 @@ Data import | GEOquery |2.52.0 Batch correction |Sva (ComBat) |3.32.1 Preprocessing, normalization, statistical analysis| Limma |3.40.6 - -Preprocessing, normalization Minfi 1.30.0 -GC-correction ArrayTV 1.22.0 -Segmenting copy number data DNAcopy 1.58.0 -Copy number calling CNVkit (Python) 0.9.6 -Genome sequences BSgenome.Hsapiens.UCSC.hg18 1.3.1 -Coordinate liftover Rtracklayer 1.44.4 -Annotation annotatr 1.10.0 -Annotation Org.Hs.eg.db 3.8.2 -Illumina identifiers lumiHumanIDMapping 1.10.1 -Identify Methylated Regions DMRcate 1.20.0 -Venn diagram -visualization VennDiagram 1.6.2 -Summarizing copy number data CNVRanger 1.0.3 -Visualize copy number data GenVisR 1.16.1 -Representation of genomic intervals GenomicRegions 1.36.1 -Data integration MixOmics 6.8.5 -Pathway analysis ReactomePA 1.28.0 -Gene set enrichment analysis gage 2.34.0 -Visualizing intersections VennDiagram 1.6.20 -Enrichment visualizations enrichplot 1.4.0 +Preprocessing, normalization| Minfi |1.30.0 +GC-correction |ArrayTV |1.22.0 +Segmenting copy number data| DNAcopy| 1.58.0 +Copy number calling |CNVkit (Python)| 0.9.6 +Genome sequences |BSgenome.Hsapiens.UCSC.hg18| 1.3.1 +Coordinate liftover |Rtracklayer |1.44.4 +Annotation |annotatr| 1.10.0 +Annotation |Org.Hs.eg.db| 3.8.2 +Illumina identifiers| lumiHumanIDMapping| 1.10.1 +Identify Methylated Regions| DMRcate| 1.20.0 +Venn diagram -visualization |VennDiagram| 1.6.2 +Summarizing copy number data |CNVRanger |1.0.3 +Visualize copy number data |GenVisR |1.16.1 +Representation of genomic intervals |GenomicRegions| 1.36.1 +Data integration |MixOmics| 6.8.5 +Pathway analysis |ReactomePA| 1.28.0 +Gene set enrichment analysis| gage |2.34.0 +Visualizing intersections |VennDiagram| 1.6.20 +Enrichment visualizations |enrichplot| 1.4.0 Gene relevance based on multiple evidences in complex networks: https://www.itb.cnr.it/mnd [Snippets] </pre> </div>Reija AutioWed, 29 Apr 2020 07:49:43 -0000https://sourceforge.netea7b9b7821dcc53b3e97c99486f53c9e75c861f3Packages modified by Reija Autiohttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v4 +++ v5 @@ -1,14 +1,7 @@ **The packages used in the GEMMA data analysis** -Description Package Version -HeaderHeader | Header | Header Description| Package | Version ---------- | ---------- | ------ -Data | Cell | Cell -Cell | Cell | Cell Header | Header | Header ----------- | ---------- | ------ -Cell | Cell | Cell -Cell | Cell | Cell Data import | GEOquery |2.52.0 Batch correction |Sva (ComBat) |3.32.1 Preprocessing, normalization, statistical analysis| Limma |3.40.6 </pre> </div>Reija AutioWed, 29 Apr 2020 07:48:16 -0000https://sourceforge.net763012f64e502e71aa306bb56285212480884408Packages modified by Reija Autiohttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v3 +++ v4 @@ -1,7 +1,18 @@ +**The packages used in the GEMMA data analysis** + Description Package Version -Data import GEOquery 2.52.0 -Batch correction Sva (ComBat) 3.32.1 -Preprocessing, normalization, statistical analysis Limma 3.40.6 +HeaderHeader | Header | Header + Description| Package | Version +---------- | ---------- | ------ +Data | Cell | Cell +Cell | Cell | Cell Header | Header | Header +---------- | ---------- | ------ +Cell | Cell | Cell +Cell | Cell | Cell +Data import | GEOquery |2.52.0 +Batch correction |Sva (ComBat) |3.32.1 +Preprocessing, normalization, statistical analysis| Limma |3.40.6 + Preprocessing, normalization Minfi 1.30.0 GC-correction ArrayTV 1.22.0 Segmenting copy number data DNAcopy 1.58.0 </pre> </div>Reija AutioWed, 29 Apr 2020 07:47:23 -0000https://sourceforge.net6946bbc04d9dbb920dd2b87dd1aebee43eb3a7fbPackages modified by Reija Autiohttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -21,5 +21,5 @@ Gene set enrichment analysis gage 2.34.0 Visualizing intersections VennDiagram 1.6.20 Enrichment visualizations enrichplot 1.4.0 -https://www.itb.cnr.it/mnd +Gene relevance based on multiple evidences in complex networks: https://www.itb.cnr.it/mnd [Snippets] </pre> </div>Reija AutioWed, 29 Apr 2020 06:25:24 -0000https://sourceforge.net80078470f65b297f3e3eff4ad9fad9fc970bd61aPackages modified by Reija Autiohttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -21,5 +21,5 @@ Gene set enrichment analysis gage 2.34.0 Visualizing intersections VennDiagram 1.6.20 Enrichment visualizations enrichplot 1.4.0 - +https://www.itb.cnr.it/mnd [Snippets] </pre> </div>Reija AutioWed, 29 Apr 2020 06:24:12 -0000https://sourceforge.netc5cffd67560f1e4c966d9879b128b2036be0eb26Packages modified by jakelinhttps://sourceforge.net/p/gemma-omics-integrate/wiki/Packages/<div class="markdown_content"><p>Description Package Version<br/> Data import GEOquery 2.52.0<br/> Batch correction Sva (ComBat) 3.32.1<br/> Preprocessing, normalization, statistical analysis Limma 3.40.6<br/> Preprocessing, normalization Minfi 1.30.0<br/> GC-correction ArrayTV 1.22.0<br/> Segmenting copy number data DNAcopy 1.58.0<br/> Copy number calling CNVkit (Python) 0.9.6<br/> Genome sequences BSgenome.Hsapiens.UCSC.hg18 1.3.1<br/> Coordinate liftover Rtracklayer 1.44.4<br/> Annotation annotatr 1.10.0<br/> Annotation Org.Hs.eg.db 3.8.2<br/> Illumina identifiers lumiHumanIDMapping 1.10.1<br/> Identify Methylated Regions DMRcate 1.20.0<br/> Venn diagram -visualization VennDiagram 1.6.2<br/> Summarizing copy number data CNVRanger 1.0.3<br/> Visualize copy number data GenVisR 1.16.1<br/> Representation of genomic intervals GenomicRegions 1.36.1<br/> Data integration MixOmics 6.8.5<br/> Pathway analysis ReactomePA 1.28.0<br/> Gene set enrichment analysis gage 2.34.0<br/> Visualizing intersections VennDiagram 1.6.20<br/> Enrichment visualizations enrichplot 1.4.0</p> <p><span>[Snippets]</span></p></div>jakelinFri, 24 Apr 2020 13:09:34 -0000https://sourceforge.net20da01b17713e5117f18214bb304d8453bd48912