EvoFuncPseudogene

Scripts used to identify the developmentally dynamic pseudogenes with functional signatures, chart their expression profile, associate them with putative functions, as well as investigate their implications in disease and cancer.

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
000.Datadownload.sh		000.Datadownload.sh
001.1.Dateage.rBestaxt.sh		001.1.Dateage.rBestaxt.sh
001.2.Dateage.Filter.R		001.2.Dateage.Filter.R
001.3.Dateage.AbundanceAge.XA.R		001.3.Dateage.AbundanceAge.XA.R
001.4.Dateage.conservation.Rmd		001.4.Dateage.conservation.Rmd
002.0.rawdata.fastqbam.Rmd		002.0.rawdata.fastqbam.Rmd
002.1.ExpressedPseu.nonredudantExon.sh		002.1.ExpressedPseu.nonredudantExon.sh
002.4.ExpressedPseu.fromallfpkm.R		002.4.ExpressedPseu.fromallfpkm.R
002.4.ExpressedPseu.phenogram.R		002.4.ExpressedPseu.phenogram.R
002.4.R1.ExpressedPseu.fromallfpkm.R		002.4.R1.ExpressedPseu.fromallfpkm.R
002.6.ExpressedPseu.genetype.R		002.6.ExpressedPseu.genetype.R
002.7.ExpressedPseu.geneage.R		002.7.ExpressedPseu.geneage.R
002.8.ExpressedPseu.UnitaryPseudoOlfactory.R		002.8.ExpressedPseu.UnitaryPseudoOlfactory.R
003.1.PCA.Human.R		003.1.PCA.Human.R
003.2.PCA.Mouse.R		003.2.PCA.Mouse.R
003.3.PCA.Human.coding.R		003.3.PCA.Human.coding.R
004.1.ExpressionSpecificity.Tissue.R		004.1.ExpressionSpecificity.Tissue.R
004.2.ExpressionSpecificity.Stage.R		004.2.ExpressionSpecificity.Stage.R
004.3.ExpressionSpecificity.pseudotype.R		004.3.ExpressionSpecificity.pseudotype.R
004.4.ExpressionSpecificity.tissuedistribution.R		004.4.ExpressionSpecificity.tissuedistribution.R
004.5.ExpressionSpecificity.Genetraffic.R		004.5.ExpressionSpecificity.Genetraffic.R
005.1.ExpressionHeterogeneity.HumanGTEx.R		005.1.ExpressionHeterogeneity.HumanGTEx.R
005.2.ExpressionHeterogeneity.Human30Tissues.R		005.2.ExpressionHeterogeneity.Human30Tissues.R
005.3.ExpressionHeterogeneity.MouseENCODE.R		005.3.ExpressionHeterogeneity.MouseENCODE.R
006.1.DDG.Human.R		006.1.DDG.Human.R
006.2.DDG.Mouse.R		006.2.DDG.Mouse.R
006.3.DDG.Number.tissue.R		006.3.DDG.Number.tissue.R
006.4.DDG.Number.expressed.tissue.time.R		006.4.DDG.Number.expressed.tissue.time.R
006.5.DDG.Number.LengthPseu.R		006.5.DDG.Number.LengthPseu.R
006.6.DDG.proportion.age.R		006.6.DDG.proportion.age.R
007.1.TranscriptionFactor.DownloadData.sh		007.1.TranscriptionFactor.DownloadData.sh
007.2.TranscriptionFactor.Promoterregion.R		007.2.TranscriptionFactor.Promoterregion.R
007.3.TranscriptionFactor.Overlap.sh		007.3.TranscriptionFactor.Overlap.sh
007.4.TranscriptionFactor.BindingNumber.R		007.4.TranscriptionFactor.BindingNumber.R
007.5.TranscriptionFactor.BindingType.R		007.5.TranscriptionFactor.BindingType.R
007.6.TranscriptionFactor.Age.R		007.6.TranscriptionFactor.Age.R
008.1.Epigenome.DownloadData.sh		008.1.Epigenome.DownloadData.sh
008.2.Epigenome.ChromHmm.overlap.sh		008.2.Epigenome.ChromHmm.overlap.sh
008.3.Epigenome.ChromHmm.visualize.R		008.3.Epigenome.ChromHmm.visualize.R
008.4.Epigenome.H3K27ac.liftoverOverlap.sh		008.4.Epigenome.H3K27ac.liftoverOverlap.sh
008.5.Epigenome.H3K27ac.visualize.R		008.5.Epigenome.H3K27ac.visualize.R
008.6.Epigenome.DHS.liftoverOverlap.sh		008.6.Epigenome.DHS.liftoverOverlap.sh
008.7.Epigenome.DHS.visualize.R		008.7.Epigenome.DHS.visualize.R
008.8.Epigenome.MouseENCODE.Download.sh		008.8.Epigenome.MouseENCODE.Download.sh
008.9.Epigenome.MouseENCODE.visualize.R		008.9.Epigenome.MouseENCODE.visualize.R
009.1.Translation.DownloadRiboseq.sh		009.1.Translation.DownloadRiboseq.sh
009.2.Translation.visualize.R		009.2.Translation.visualize.R
009.3.Translation.CPC2CPAT.Rmd		009.3.Translation.CPC2CPAT.Rmd
009.4.R1.Translation.Rmd		009.4.R1.Translation.Rmd
010.1.ExpressionCorrelation.ClosestCoding.R		010.1.ExpressionCorrelation.ClosestCoding.R
010.2.ExpressionCorrelation.Coexpression.R		010.2.ExpressionCorrelation.Coexpression.R
010.3.ExpressionCorrelation.CompareDDG.R		010.3.ExpressionCorrelation.CompareDDG.R
010.4.ExpressionCorrelation.Circos.R		010.4.ExpressionCorrelation.Circos.R
011.1.TE.DownloadData.sh		011.1.TE.DownloadData.sh
011.2.TE.GeneType.R		011.2.TE.GeneType.R
012.1.GWAS.GWAS.Rmd		012.1.GWAS.GWAS.Rmd
013.1.PTregulation.RBPM6A.Rmd		013.1.PTregulation.RBPM6A.Rmd
014.1.TCGA.DownloadData.R		014.1.TCGA.DownloadData.R
014.2.TCGA.LineageSpecific.R		014.2.TCGA.LineageSpecific.R
014.3.TCGA.DEG.R		014.3.TCGA.DEG.R
014.4.TCGA.IntersectLineageDEG.R		014.4.TCGA.IntersectLineageDEG.R
014.5.TCGA.DEGoverlapwithinCancerType.R		014.5.TCGA.DEGoverlapwithinCancerType.R
014.6.TCGA.DEGoverlapwithDDG.R		014.6.TCGA.DEGoverlapwithDDG.R
015.1.ImmuPseudo.Test.R		015.1.ImmuPseudo.Test.R
015.2.ImmuPseudo.ComRNA4TurPur.R		015.2.ImmuPseudo.ComRNA4TurPur.R
015.3.ImmuPseudo.ImmuPseudo.R		015.3.ImmuPseudo.ImmuPseudo.R
015.4.ImmuPseudo.ImmuPseudoVisual.R		015.4.ImmuPseudo.ImmuPseudoVisual.R
015.5.ImmuPseudo.InfiltrationPseudo.R		015.5.ImmuPseudo.InfiltrationPseudo.R
015.6.ImmuPseudo.ImmuOverlapInfiltrate.R		015.6.ImmuPseudo.ImmuOverlapInfiltrate.R
LICENSE		LICENSE
README.md		README.md
S001.1.DEG.fisrtref.adjacent.R		S001.1.DEG.fisrtref.adjacent.R
S001.2.DEG.visual.adjacent.R		S001.2.DEG.visual.adjacent.R
S001.3.DEG.visual.4wpcref.R		S001.3.DEG.visual.4wpcref.R
S002.1.ATAC.download.sh		S002.1.ATAC.download.sh
S003.1.RICseq.R		S003.1.RICseq.R
S003.1.Sexbias.Sexbias.R		S003.1.Sexbias.Sexbias.R
S004.1.DevelopmentAge.ExpressedPseudo.R		S004.1.DevelopmentAge.ExpressedPseudo.R
S005.1.ParentcodingCharacter.R		S005.1.ParentcodingCharacter.R
S006.1.NewCount.Merge.R		S006.1.NewCount.Merge.R
S006.2.PacBio.Rmd		S006.2.PacBio.Rmd
S007.1.Conservation.R		S007.1.Conservation.R

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