├── !old.to.remove.devAS.R ├── .Rhistory ├── 2018.06.26.Q-n-A.R ├── MDSs.R ├── ad.on.ge.R ├── age.aligned.R ├── alternification.R ├── as.on.age.R ├── chain.from.Ray ├── README ├── align.mouse.chr1.rat.chr1.sh ├── chain.liftover.sh ├── chain.liftover.swap.sh ├── generate.bsub.scripts.sh ├── send.lastz.sh ├── substitution.matrix └── swap.chains.sh ├── check.introns.R ├── comp.read.counts.R ├── cov.bias.R ├── devAS.R ├── hexamers.R ├── hqm.subsampling.R ├── hqmrboc.subsampling.R ├── hqmrboc.subsampling.cluster.R ├── japan.embrios.R ├── lncRNA.R ├── load.all.data.R ├── mark.antisense.duplicates.R ├── microexons.R ├── new.exons.R ├── newborn.exons.plot.cov.R ├── not.r ├── .Rhistory ├── .ipynb_checkpoints │ └── myGPClust-checkpoint.ipynb ├── bam2fq │ ├── bam2fq.all.sh │ ├── bam2fq.all.sh~ │ ├── bam2fq.jar │ ├── bam2fq.sh │ ├── bam2fq.sh~ │ ├── comp2fastq.pl │ └── remove.fastq.dupl.pl ├── extract.ad.seq.sh ├── extract.seq.of.spl.sites.py ├── extractSeqFromFasta.pl ├── extractSeqFromFasta.py ├── extractSeqFromFasta.py~ ├── getConsFromWig.py ├── getConsFromWig.py~ ├── getSNPfromVCF.py ├── getSNPfromVCF.py~ ├── hisat2.chi.je.run.sh ├── hisat2.chimp.testis.run.sh ├── hisat2.mou.je.run.sh ├── hisat2.qki.rnai.run.sh ├── hqm.subsetting.make.orth.segments.py ├── hqmrboc.subsampling.cluster.sh ├── liftover.annotations.py ├── liftover.hqm.subsample.annotations.py ├── liftover.hqm.subsample.annotations.sh ├── liftover.hqmrboc.subsample.annotations.py ├── liftover.hqmrboc.subsample.annotations.sh ├── liftover.junctions.py ├── liftover.junctions.py~ ├── make.junction.liftover.sh ├── make.junction.liftover.sh~ ├── make.orth.segments.py ├── make.orth.segments.py~ ├── map.f.hisat2.f.run.sh ├── map.f.run.all.mapping ├── merge.first.ann.liftovers.sh ├── merge.lo.py ├── merge.lo.py~ ├── merge.species.splicesites.sh ├── merge.species.splicesites.sh~ ├── myGPClust.ipynb ├── parse.hisat.logs.pl ├── run.cov.bias.sh └── run.plot.newborn.cov.sh ├── paper.figures.1.R ├── paper.figures.3.2.R ├── paper.figures.3.R ├── paper.figures.4.R ├── paper.figures.5.R ├── paper.figures.R ├── qki.R ├── r.functions ├── ad.on.ge.F.R ├── ageAlignment.R ├── as.on.age.F.R ├── check.introns.F.R ├── clustering.per.tissue.F.R ├── load.all.data.F.R ├── paper.figures.4.F.R ├── paper.figures.5.F.R ├── paper.figures.F.R ├── ssPWM.F.R └── time.scale.F.R ├── shiny ├── mar.app.2020.R ├── mar.app.R ├── mar.helpers.R ├── prepare.data.R └── www │ ├── Mammalian_evolutionTransparent.png │ ├── scripts.js │ └── styles.css ├── shuny ├── mar.app.R ├── mar.helpers.R └── prepare.data.R ├── sp.pattern.changes.R ├── titin.R └── what.is.wrong.with.human.8wpc.R /!old.to.remove.devAS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iaaaka/evo-devo/HEAD/!old.to.remove.devAS.R -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- 1 | 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