Files in wikiselev/rnaseq.mcf10a
Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

DESCRIPTION

NAMESPACE

R/clust.R R/data.R R/diff-expr.R R/plot.R README.md data-raw/checks.R data-raw/clust.R data-raw/count-matrix.R data-raw/diff-expr.R data-raw/gene-ann.R data-raw/go-plot.R data-raw/go.R data-raw/initial-sets.R data-raw/ismara.R

data-raw/kiselev-pip3-rna-seq-gene-profiles/data/exon-map-lengths.csv

data-raw/kiselev-pip3-rna-seq-gene-profiles/data/plot-data.rds

data-raw/kiselev-pip3-rna-seq-gene-profiles/server.R data-raw/kiselev-pip3-rna-seq-gene-profiles/ui.R data-raw/main.R data-raw/other-data.R data-raw/plot-table.R data-raw/proteomics.R

data-raw/raw-processing.txt

data-raw/revigo.py

data/auxiliary.gene.sets.rda

data/count.data.table.rda

data/count.matrix.rda

data/count.matrix.rpkm.rda

data/count.matrix.scaled.rda

data/diff.expr.all.rda

data/gene.annotations.rda

data/gene.clusters.all.rda

data/gene.sets.GO.rda

data/ismara.targets.rda

data/main.gene.sets.rda

data/plot.data.rda

data/plot.data.rpkm.rda

data/plot.data.scaled.rda

data/prdm1.targets.rda

inst/extdata/GO/set1-1/BP-Fisher-revigo.txt

inst/extdata/GO/set1-1/REVIGO.csv

inst/extdata/GO/set1-1/genes-ann-BP.rds

inst/extdata/GO/set1-1/revigo_treemap.pdf inst/extdata/GO/set1-1/treemap.R

inst/extdata/GO/set1-2/BP-Fisher-revigo.txt

inst/extdata/GO/set1-2/REVIGO.csv

inst/extdata/GO/set1-2/genes-ann-BP.rds

inst/extdata/GO/set1-2/revigo_treemap.pdf inst/extdata/GO/set1-2/treemap.R

inst/extdata/GO/set1/BP-Fisher-revigo.txt

inst/extdata/GO/set1/REVIGO.csv

inst/extdata/GO/set1/genes-ann-BP.rds

inst/extdata/GO/set1/revigo_treemap.pdf inst/extdata/GO/set1/treemap.R

inst/extdata/GO/set2-1/BP-Fisher-revigo.txt

inst/extdata/GO/set2-1/REVIGO.csv

inst/extdata/GO/set2-1/genes-ann-BP.rds

inst/extdata/GO/set2-1/revigo_treemap.pdf inst/extdata/GO/set2-1/treemap.R

inst/extdata/GO/set2-2/BP-Fisher-revigo.txt

inst/extdata/GO/set2-2/REVIGO.csv

inst/extdata/GO/set2-2/genes-ann-BP.rds

inst/extdata/GO/set2-2/revigo_treemap.pdf inst/extdata/GO/set2-2/treemap.R

inst/extdata/GO/set2-3/BP-Fisher-revigo.txt

inst/extdata/GO/set2-3/REVIGO.csv

inst/extdata/GO/set2-3/genes-ann-BP.rds

inst/extdata/GO/set2-3/revigo_treemap.pdf inst/extdata/GO/set2-3/treemap.R

inst/extdata/GO/set2-4/BP-Fisher-revigo.txt

inst/extdata/GO/set2-4/REVIGO.csv

inst/extdata/GO/set2-4/genes-ann-BP.rds

inst/extdata/GO/set2-4/revigo_treemap.pdf inst/extdata/GO/set2-4/treemap.R

inst/extdata/GO/set2/BP-Fisher-revigo.txt

inst/extdata/GO/set2/REVIGO.csv

inst/extdata/GO/set2/genes-ann-BP.rds

inst/extdata/GO/set2/revigo_treemap.pdf inst/extdata/GO/set2/treemap.R

inst/extdata/GO/set3-1/BP-Fisher-revigo.txt

inst/extdata/GO/set3-1/REVIGO.csv

inst/extdata/GO/set3-1/genes-ann-BP.rds

inst/extdata/GO/set3-1/revigo_treemap.pdf inst/extdata/GO/set3-1/treemap.R

inst/extdata/GO/set3-2/BP-Fisher-revigo.txt

inst/extdata/GO/set3-2/REVIGO.csv

inst/extdata/GO/set3-2/genes-ann-BP.rds

inst/extdata/GO/set3-2/revigo_treemap.pdf inst/extdata/GO/set3-2/treemap.R

inst/extdata/GO/set3/BP-Fisher-revigo.txt

inst/extdata/GO/set3/REVIGO.csv

inst/extdata/GO/set3/genes-ann-BP.rds

inst/extdata/GO/set3/revigo_treemap.pdf inst/extdata/GO/set3/treemap.R

inst/extdata/GO/set4-1/BP-Fisher-revigo.txt

inst/extdata/GO/set4-1/REVIGO.csv

inst/extdata/GO/set4-1/genes-ann-BP.rds

inst/extdata/GO/set4-1/revigo_treemap.pdf inst/extdata/GO/set4-1/treemap.R

inst/extdata/GO/set4-2/BP-Fisher-revigo.txt

inst/extdata/GO/set4-2/REVIGO.csv

inst/extdata/GO/set4-2/genes-ann-BP.rds

inst/extdata/GO/set4-2/revigo_treemap.pdf inst/extdata/GO/set4-2/treemap.R

inst/extdata/GO/set4-3/BP-Fisher-revigo.txt

inst/extdata/GO/set4-3/REVIGO.csv

inst/extdata/GO/set4-3/genes-ann-BP.rds

inst/extdata/GO/set4-3/revigo_treemap.pdf inst/extdata/GO/set4-3/treemap.R

inst/extdata/GO/set4-4/BP-Fisher-revigo.txt

inst/extdata/GO/set4-4/REVIGO.csv

inst/extdata/GO/set4-4/genes-ann-BP.rds

inst/extdata/GO/set4-4/revigo_treemap.pdf inst/extdata/GO/set4-4/treemap.R

inst/extdata/GO/set4/BP-Fisher-revigo.txt

inst/extdata/GO/set4/REVIGO.csv

inst/extdata/GO/set4/genes-ann-BP.rds

inst/extdata/GO/set4/revigo_treemap.pdf inst/extdata/GO/set4/treemap.R

inst/extdata/GO/set5-1/BP-Fisher-revigo.txt

inst/extdata/GO/set5-1/REVIGO.csv

inst/extdata/GO/set5-1/genes-ann-BP.rds

inst/extdata/GO/set5-1/revigo_treemap.pdf inst/extdata/GO/set5-1/treemap.R

inst/extdata/GO/set5-2/BP-Fisher-revigo.txt

inst/extdata/GO/set5-2/REVIGO.csv

inst/extdata/GO/set5-2/genes-ann-BP.rds

inst/extdata/GO/set5-2/revigo_treemap.pdf inst/extdata/GO/set5-2/treemap.R

inst/extdata/GO/set5/BP-Fisher-revigo.txt

inst/extdata/GO/set5/REVIGO.csv

inst/extdata/GO/set5/genes-ann-BP.rds

inst/extdata/GO/set5/revigo_treemap.pdf inst/extdata/GO/set5/treemap.R

inst/extdata/GO/set6-1/BP-Fisher-revigo.txt

inst/extdata/GO/set6-1/REVIGO.csv

inst/extdata/GO/set6-1/genes-ann-BP.rds

inst/extdata/GO/set6-1/revigo_treemap.pdf inst/extdata/GO/set6-1/treemap.R

inst/extdata/GO/set6-2/BP-Fisher-revigo.txt

inst/extdata/GO/set6-2/REVIGO.csv

inst/extdata/GO/set6-2/genes-ann-BP.rds

inst/extdata/GO/set6-2/revigo_treemap.pdf inst/extdata/GO/set6-2/treemap.R

inst/extdata/GO/set6/BP-Fisher-revigo.txt

inst/extdata/GO/set6/REVIGO.csv

inst/extdata/GO/set6/genes-ann-BP.rds

inst/extdata/GO/set6/revigo_treemap.pdf inst/extdata/GO/set6/treemap.R

inst/extdata/GO/setA-1/BP-Fisher-revigo.txt

inst/extdata/GO/setA-1/REVIGO.csv

inst/extdata/GO/setA-1/genes-ann-BP.rds

inst/extdata/GO/setA-1/revigo_treemap.pdf inst/extdata/GO/setA-1/treemap.R

inst/extdata/GO/setA-2/BP-Fisher-revigo.txt

inst/extdata/GO/setA-2/REVIGO.csv

inst/extdata/GO/setA-2/genes-ann-BP.rds

inst/extdata/GO/setA-2/revigo_treemap.pdf inst/extdata/GO/setA-2/treemap.R

inst/extdata/GO/setA-3/BP-Fisher-revigo.txt

inst/extdata/GO/setA-3/REVIGO.csv

inst/extdata/GO/setA-3/genes-ann-BP.rds

inst/extdata/GO/setA-3/revigo_treemap.pdf inst/extdata/GO/setA-3/treemap.R

inst/extdata/GO/setA-4/BP-Fisher-revigo.txt

inst/extdata/GO/setA-4/REVIGO.csv

inst/extdata/GO/setA-4/genes-ann-BP.rds

inst/extdata/GO/setA-4/revigo_treemap.pdf inst/extdata/GO/setA-4/treemap.R

inst/extdata/GO/setA-5/BP-Fisher-revigo.txt

inst/extdata/GO/setA-5/REVIGO.csv

inst/extdata/GO/setA-5/genes-ann-BP.rds

inst/extdata/GO/setA-5/revigo_treemap.pdf inst/extdata/GO/setA-5/treemap.R

inst/extdata/GO/setA/BP-Fisher-revigo.txt

inst/extdata/GO/setA/REVIGO.csv

inst/extdata/GO/setA/genes-ann-BP.rds

inst/extdata/GO/setA/revigo_treemap.pdf inst/extdata/GO/setA/treemap.R

inst/extdata/GO/setB-1/BP-Fisher-revigo.txt

inst/extdata/GO/setB-1/REVIGO.csv

inst/extdata/GO/setB-1/genes-ann-BP.rds

inst/extdata/GO/setB-1/revigo_treemap.pdf inst/extdata/GO/setB-1/treemap.R

inst/extdata/GO/setB-2/BP-Fisher-revigo.txt

inst/extdata/GO/setB-2/REVIGO.csv

inst/extdata/GO/setB-2/genes-ann-BP.rds

inst/extdata/GO/setB-2/revigo_treemap.pdf inst/extdata/GO/setB-2/treemap.R

inst/extdata/GO/setB-3/BP-Fisher-revigo.txt

inst/extdata/GO/setB-3/REVIGO.csv

inst/extdata/GO/setB-3/genes-ann-BP.rds

inst/extdata/GO/setB-3/revigo_treemap.pdf inst/extdata/GO/setB-3/treemap.R

inst/extdata/GO/setB-4/BP-Fisher-revigo.txt

inst/extdata/GO/setB-4/REVIGO.csv

inst/extdata/GO/setB-4/genes-ann-BP.rds

inst/extdata/GO/setB-4/revigo_treemap.pdf inst/extdata/GO/setB-4/treemap.R

inst/extdata/GO/setB/BP-Fisher-revigo.txt

inst/extdata/GO/setB/REVIGO.csv

inst/extdata/GO/setB/genes-ann-BP.rds

inst/extdata/GO/setB/revigo_treemap.pdf inst/extdata/GO/setB/treemap.R

inst/extdata/GO/setC-1/BP-Fisher-revigo.txt

inst/extdata/GO/setC-1/REVIGO.csv

inst/extdata/GO/setC-1/genes-ann-BP.rds

inst/extdata/GO/setC-1/revigo_treemap.pdf inst/extdata/GO/setC-1/treemap.R

inst/extdata/GO/setC-2/BP-Fisher-revigo.txt

inst/extdata/GO/setC-2/REVIGO.csv

inst/extdata/GO/setC-2/genes-ann-BP.rds

inst/extdata/GO/setC-2/revigo_treemap.pdf inst/extdata/GO/setC-2/treemap.R

inst/extdata/GO/setC-3/BP-Fisher-revigo.txt

inst/extdata/GO/setC-3/REVIGO.csv

inst/extdata/GO/setC-3/genes-ann-BP.rds

inst/extdata/GO/setC-3/revigo_treemap.pdf inst/extdata/GO/setC-3/treemap.R

inst/extdata/GO/setC/BP-Fisher-revigo.txt

inst/extdata/GO/setC/REVIGO.csv

inst/extdata/GO/setC/genes-ann-BP.rds

inst/extdata/GO/setC/revigo_treemap.pdf inst/extdata/GO/setC/treemap.R

inst/extdata/GO/setD-1/BP-Fisher-revigo.txt

inst/extdata/GO/setD-1/REVIGO.csv

inst/extdata/GO/setD-1/genes-ann-BP.rds

inst/extdata/GO/setD-1/revigo_treemap.pdf inst/extdata/GO/setD-1/treemap.R

inst/extdata/GO/setD-2/BP-Fisher-revigo.txt

inst/extdata/GO/setD-2/REVIGO.csv

inst/extdata/GO/setD-2/genes-ann-BP.rds

inst/extdata/GO/setD-2/revigo_treemap.pdf inst/extdata/GO/setD-2/treemap.R

inst/extdata/GO/setD/BP-Fisher-revigo.txt

inst/extdata/GO/setD/REVIGO.csv

inst/extdata/GO/setD/genes-ann-BP.rds

inst/extdata/GO/setD/revigo_treemap.pdf inst/extdata/GO/setD/treemap.R

inst/extdata/GO/setE-1/BP-Fisher-revigo.txt

inst/extdata/GO/setE-1/REVIGO.csv

inst/extdata/GO/setE-1/genes-ann-BP.rds

inst/extdata/GO/setE-1/revigo_treemap.pdf inst/extdata/GO/setE-1/treemap.R

inst/extdata/GO/setE-2/BP-Fisher-revigo.txt

inst/extdata/GO/setE-2/REVIGO.csv

inst/extdata/GO/setE-2/genes-ann-BP.rds

inst/extdata/GO/setE-2/revigo_treemap.pdf inst/extdata/GO/setE-2/treemap.R

inst/extdata/GO/setE-3/BP-Fisher-revigo.txt

inst/extdata/GO/setE-3/REVIGO.csv

inst/extdata/GO/setE-3/genes-ann-BP.rds

inst/extdata/GO/setE-3/revigo_treemap.pdf inst/extdata/GO/setE-3/treemap.R

inst/extdata/GO/setE-4/BP-Fisher-revigo.txt

inst/extdata/GO/setE-4/REVIGO.csv

inst/extdata/GO/setE-4/genes-ann-BP.rds

inst/extdata/GO/setE-4/revigo_treemap.pdf inst/extdata/GO/setE-4/treemap.R

inst/extdata/GO/setE-5/BP-Fisher-revigo.txt

inst/extdata/GO/setE-5/REVIGO.csv

inst/extdata/GO/setE-5/genes-ann-BP.rds

inst/extdata/GO/setE-5/revigo_treemap.pdf inst/extdata/GO/setE-5/treemap.R

inst/extdata/GO/setE/BP-Fisher-revigo.txt

inst/extdata/GO/setE/REVIGO.csv

inst/extdata/GO/setE/genes-ann-BP.rds

inst/extdata/GO/setE/revigo_treemap.pdf inst/extdata/GO/setE/treemap.R

inst/extdata/GO/setF-1/BP-Fisher-revigo.txt

inst/extdata/GO/setF-1/REVIGO.csv

inst/extdata/GO/setF-1/genes-ann-BP.rds

inst/extdata/GO/setF-1/revigo_treemap.pdf inst/extdata/GO/setF-1/treemap.R

inst/extdata/GO/setF-2/BP-Fisher-revigo.txt

inst/extdata/GO/setF-2/REVIGO.csv

inst/extdata/GO/setF-2/genes-ann-BP.rds

inst/extdata/GO/setF-2/revigo_treemap.pdf inst/extdata/GO/setF-2/treemap.R

inst/extdata/GO/setF/BP-Fisher-revigo.txt

inst/extdata/GO/setF/REVIGO.csv

inst/extdata/GO/setF/genes-ann-BP.rds

inst/extdata/GO/setF/revigo_treemap.pdf inst/extdata/GO/setF/treemap.R

inst/extdata/GO/setG-1/BP-Fisher-revigo.txt

inst/extdata/GO/setG-1/REVIGO.csv

inst/extdata/GO/setG-1/genes-ann-BP.rds

inst/extdata/GO/setG-1/revigo_treemap.pdf inst/extdata/GO/setG-1/treemap.R

inst/extdata/GO/setG-2/BP-Fisher-revigo.txt

inst/extdata/GO/setG-2/REVIGO.csv

inst/extdata/GO/setG-2/genes-ann-BP.rds

inst/extdata/GO/setG-2/revigo_treemap.pdf inst/extdata/GO/setG-2/treemap.R

inst/extdata/GO/setG-3/BP-Fisher-revigo.txt

inst/extdata/GO/setG-3/REVIGO.csv

inst/extdata/GO/setG-3/genes-ann-BP.rds

inst/extdata/GO/setG-3/revigo_treemap.pdf inst/extdata/GO/setG-3/treemap.R

inst/extdata/GO/setG-4/BP-Fisher-revigo.txt

inst/extdata/GO/setG-4/REVIGO.csv

inst/extdata/GO/setG-4/genes-ann-BP.rds

inst/extdata/GO/setG-4/revigo_treemap.pdf inst/extdata/GO/setG-4/treemap.R

inst/extdata/GO/setG/BP-Fisher-revigo.txt

inst/extdata/GO/setG/REVIGO.csv

inst/extdata/GO/setG/genes-ann-BP.rds

inst/extdata/GO/setG/revigo_treemap.pdf inst/extdata/GO/setG/treemap.R

inst/extdata/GO/setH-1/BP-Fisher-revigo.txt

inst/extdata/GO/setH-1/REVIGO.csv

inst/extdata/GO/setH-1/genes-ann-BP.rds

inst/extdata/GO/setH-1/revigo_treemap.pdf inst/extdata/GO/setH-1/treemap.R

inst/extdata/GO/setH-2/BP-Fisher-revigo.txt

inst/extdata/GO/setH-2/REVIGO.csv

inst/extdata/GO/setH-2/genes-ann-BP.rds

inst/extdata/GO/setH-2/revigo_treemap.pdf inst/extdata/GO/setH-2/treemap.R

inst/extdata/GO/setH-3/BP-Fisher-revigo.txt

inst/extdata/GO/setH-3/REVIGO.csv

inst/extdata/GO/setH-3/genes-ann-BP.rds

inst/extdata/GO/setH-3/revigo_treemap.pdf inst/extdata/GO/setH-3/treemap.R

inst/extdata/GO/setH/BP-Fisher-revigo.txt

inst/extdata/GO/setH/REVIGO.csv

inst/extdata/GO/setH/genes-ann-BP.rds

inst/extdata/GO/setH/revigo_treemap.pdf inst/extdata/GO/setH/treemap.R

inst/extdata/clusts/set1-2.rds

inst/extdata/clusts/set1-3.rds

inst/extdata/clusts/set1-4.rds

inst/extdata/clusts/set1-5.rds

inst/extdata/clusts/set1-6.rds

inst/extdata/clusts/set2-2.rds

inst/extdata/clusts/set2-3.rds

inst/extdata/clusts/set2-4.rds

inst/extdata/clusts/set2-5.rds

inst/extdata/clusts/set2-6.rds

inst/extdata/clusts/set3-2.rds

inst/extdata/clusts/set3-3.rds

inst/extdata/clusts/set3-4.rds

inst/extdata/clusts/set3-5.rds

inst/extdata/clusts/set3-6.rds

inst/extdata/clusts/set4-2.rds

inst/extdata/clusts/set4-3.rds

inst/extdata/clusts/set4-4.rds

inst/extdata/clusts/set4-5.rds

inst/extdata/clusts/set4-6.rds

inst/extdata/clusts/set5-2.rds

inst/extdata/clusts/set5-3.rds

inst/extdata/clusts/set5-4.rds

inst/extdata/clusts/set5-5.rds

inst/extdata/clusts/set5-6.rds

inst/extdata/clusts/set6-2.rds

inst/extdata/clusts/set6-3.rds

inst/extdata/clusts/set6-4.rds

inst/extdata/clusts/set6-5.rds

inst/extdata/clusts/set6-6.rds

inst/extdata/clusts/setA-2.rds

inst/extdata/clusts/setA-3.rds

inst/extdata/clusts/setA-4.rds

inst/extdata/clusts/setA-5.rds

inst/extdata/clusts/setA-6.rds

inst/extdata/clusts/setA-7.rds

inst/extdata/clusts/setB-2.rds

inst/extdata/clusts/setB-3.rds

inst/extdata/clusts/setB-4.rds

inst/extdata/clusts/setB-5.rds

inst/extdata/clusts/setB-6.rds

inst/extdata/clusts/setC-2.rds

inst/extdata/clusts/setC-3.rds

inst/extdata/clusts/setC-4.rds

inst/extdata/clusts/setC-5.rds

inst/extdata/clusts/setC-6.rds

inst/extdata/clusts/setC-7.rds

inst/extdata/clusts/setD-2.rds

inst/extdata/clusts/setD-3.rds

inst/extdata/clusts/setD-4.rds

inst/extdata/clusts/setD-5.rds

inst/extdata/clusts/setD-6.rds

inst/extdata/clusts/setE-2.rds

inst/extdata/clusts/setE-3.rds

inst/extdata/clusts/setE-4.rds

inst/extdata/clusts/setE-5.rds

inst/extdata/clusts/setE-6.rds

inst/extdata/clusts/setE-7.rds

inst/extdata/clusts/setF-2.rds

inst/extdata/clusts/setF-3.rds

inst/extdata/clusts/setF-4.rds

inst/extdata/clusts/setF-5.rds

inst/extdata/clusts/setF-6.rds

inst/extdata/clusts/setG-2.rds

inst/extdata/clusts/setG-3.rds

inst/extdata/clusts/setG-4.rds

inst/extdata/clusts/setG-5.rds

inst/extdata/clusts/setG-6.rds

inst/extdata/clusts/setG-7.rds

inst/extdata/clusts/setH-2.rds

inst/extdata/clusts/setH-3.rds

inst/extdata/clusts/setH-4.rds

inst/extdata/clusts/setH-5.rds

inst/extdata/clusts/setH-6.rds

inst/extdata/gene-ann-illumina/exon.lengths.csv

inst/extdata/htseq/ki_1_0_trimmed_sn.sam.count

inst/extdata/htseq/ki_1_15_trimmed_sn.sam.count

inst/extdata/htseq/ki_1_180_trimmed_sn.sam.count

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inst/extdata/htseq/ki_2_15_trimmed_sn.sam.count

inst/extdata/htseq/ki_2_180_trimmed_sn.sam.count

inst/extdata/htseq/ki_2_300_trimmed_sn.sam.count

inst/extdata/htseq/ki_2_40_trimmed_sn.sam.count

inst/extdata/htseq/ki_2_90_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_0_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_15_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_180_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_300_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_40_trimmed_sn.sam.count

inst/extdata/htseq/ki_3_90_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_0_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_15_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_180_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_300_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_40_trimmed_sn.sam.count

inst/extdata/htseq/ko_2_90_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_0_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_15_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_180_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_300_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_40_trimmed_sn.sam.count

inst/extdata/htseq/ko_3_90_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_0_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_15_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_180_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_300_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_40_trimmed_sn.sam.count

inst/extdata/htseq/ko_4_90_trimmed_sn.sam.count

inst/extdata/htseq/konost_1_300_trimmed_sn.sam.count

inst/extdata/htseq/konost_2_300_trimmed_sn.sam.count

inst/extdata/htseq/konost_3_300_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_0_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_15_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_180_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_300_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_40_trimmed_sn.sam.count

inst/extdata/htseq/pten_2_90_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_0_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_15_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_180_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_300_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_40_trimmed_sn.sam.count

inst/extdata/htseq/pten_3_90_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_0_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_15_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_180_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_300_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_40_trimmed_sn.sam.count

inst/extdata/htseq/pten_4_90_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_0_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_15_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_180_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_300_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_40_trimmed_sn.sam.count

inst/extdata/htseq/wt_2_90_trimmed_sn.sam.count

inst/extdata/htseq/wt_3_15_trimmed_sn.sam.count

inst/extdata/htseq/wt_3_180_trimmed_sn.sam.count

inst/extdata/htseq/wt_3_300_trimmed_sn.sam.count

inst/extdata/htseq/wt_3_90_trimmed_sn.sam.count

inst/extdata/htseq/wt_3b_0_trimmed_sn.sam.count

inst/extdata/htseq/wt_3b_40_trimmed_sn.sam.count

inst/extdata/htseq/wt_4_0_trimmed_sn.sam.count

inst/extdata/htseq/wt_4_15_trimmed_sn.sam.count

inst/extdata/htseq/wt_4_180_trimmed_sn.sam.count

inst/extdata/htseq/wt_4_300_trimmed_sn.sam.count

inst/extdata/htseq/wt_4_90_trimmed_sn.sam.count

inst/extdata/htseq/wt_4b_40_trimmed_sn.sam.count

inst/extdata/ismara/active_matrices.txt

inst/extdata/ismara/activity_table.txt

inst/extdata/ismara/delta_table.txt

inst/extdata/ismara/targets/AAAGUGC.txt

inst/extdata/ismara/targets/AACACUG.txt

inst/extdata/ismara/targets/AACAGUC.txt

inst/extdata/ismara/targets/AACCGUU.txt

inst/extdata/ismara/targets/AACCUGG.txt

inst/extdata/ismara/targets/AACGGAA.txt

inst/extdata/ismara/targets/AAGGCAC.txt

inst/extdata/ismara/targets/AAGGUGC.txt

inst/extdata/ismara/targets/AAGUGCU.txt

inst/extdata/ismara/targets/AAUACUG.txt

inst/extdata/ismara/targets/AAUCUCA.txt

inst/extdata/ismara/targets/AAUCUCU.txt

inst/extdata/ismara/targets/AAUGCCC.txt

inst/extdata/ismara/targets/ACAGUAC.txt

inst/extdata/ismara/targets/ACAGUAU.txt

inst/extdata/ismara/targets/ACAUUCA.txt

inst/extdata/ismara/targets/ACCCGUA.txt

inst/extdata/ismara/targets/ACCCUGU.txt

inst/extdata/ismara/targets/ACUGCAU.txt

inst/extdata/ismara/targets/ACUGGCC.txt

inst/extdata/ismara/targets/ADNP_IRX_SIX_ZHX.p2.txt

inst/extdata/ismara/targets/AGCACCA.txt

inst/extdata/ismara/targets/AGCAGCA.txt

inst/extdata/ismara/targets/AGCAGCG.txt

inst/extdata/ismara/targets/AGCUGCC.txt

inst/extdata/ismara/targets/AGCUUAU.txt

inst/extdata/ismara/targets/AGGUAGU.txt

inst/extdata/ismara/targets/AGUGCAA.txt

inst/extdata/ismara/targets/AGUGGUU.txt

inst/extdata/ismara/targets/AHR_ARNT_ARNT2.p2.txt

inst/extdata/ismara/targets/AIRE.p2.txt

inst/extdata/ismara/targets/ALX1.p2.txt

inst/extdata/ismara/targets/AR.p2.txt

inst/extdata/ismara/targets/ARID5B.p2.txt

inst/extdata/ismara/targets/ARNT_ARNT2_BHLHB2_MAX_MYC_USF1.p2.txt

inst/extdata/ismara/targets/ATF2.p2.txt

inst/extdata/ismara/targets/ATF4.p2.txt

inst/extdata/ismara/targets/ATF5_CREB3.p2.txt

inst/extdata/ismara/targets/ATF6.p2.txt

inst/extdata/ismara/targets/AUGACAC.txt

inst/extdata/ismara/targets/AUGGCAC.txt

inst/extdata/ismara/targets/AUGGCUU.txt

inst/extdata/ismara/targets/AUGUGCC.txt

inst/extdata/ismara/targets/AUUGCAC.txt

inst/extdata/ismara/targets/BACH2.p2.txt

inst/extdata/ismara/targets/BPTF.p2.txt

inst/extdata/ismara/targets/CACAGUG.txt

inst/extdata/ismara/targets/CAGCAGG.txt

inst/extdata/ismara/targets/CAGUGCA.txt

inst/extdata/ismara/targets/CCAGCAU.txt

inst/extdata/ismara/targets/CCAGUGU.txt

inst/extdata/ismara/targets/CCCUGAG.txt

inst/extdata/ismara/targets/CCUUCAU.txt

inst/extdata/ismara/targets/CDC5L.p2.txt

inst/extdata/ismara/targets/CDX1,2,4.p2.txt

inst/extdata/ismara/targets/CEBPA,B_DDIT3.p2.txt

inst/extdata/ismara/targets/CGUACCG.txt

inst/extdata/ismara/targets/CGUGUCU.txt

inst/extdata/ismara/targets/CREB1.p2.txt

inst/extdata/ismara/targets/CRX.p2.txt

inst/extdata/ismara/targets/CTCF.p2.txt

inst/extdata/ismara/targets/CUACAGU.txt

inst/extdata/ismara/targets/CUCCCAA.txt

inst/extdata/ismara/targets/CUUUGGU.txt

inst/extdata/ismara/targets/CUX2.p2.txt

inst/extdata/ismara/targets/DBP.p2.txt

inst/extdata/ismara/targets/DMAP1_NCOR{1,2}_SMARC.p2.txt

inst/extdata/ismara/targets/E2F1..5.p2.txt

inst/extdata/ismara/targets/EBF1.p2.txt

inst/extdata/ismara/targets/EGR1..3.p2.txt

inst/extdata/ismara/targets/EHF.p2.txt

inst/extdata/ismara/targets/ELF1,2,4.p2.txt

inst/extdata/ismara/targets/ELK1,4_GABP{A,B1}.p3.txt

inst/extdata/ismara/targets/EN1,2.p2.txt

inst/extdata/ismara/targets/EOMES.p2.txt

inst/extdata/ismara/targets/EP300.p2.txt

inst/extdata/ismara/targets/ESR1.p2.txt

inst/extdata/ismara/targets/ESRRA.p2.txt

inst/extdata/ismara/targets/ETS1,2.p2.txt

inst/extdata/ismara/targets/EVI1.p2.txt

inst/extdata/ismara/targets/EWSR1-FLI1.p2.txt

inst/extdata/ismara/targets/FEV.p2.txt

inst/extdata/ismara/targets/FOSL2.p2.txt

inst/extdata/ismara/targets/FOS_FOS{B,L1}_JUN{B,D}.p2.txt

inst/extdata/ismara/targets/FOXA2.p3.txt

inst/extdata/ismara/targets/FOXD3.p2.txt

inst/extdata/ismara/targets/FOXL1.p2.txt

inst/extdata/ismara/targets/FOXN1.p2.txt

inst/extdata/ismara/targets/FOXO1,3,4.p2.txt

inst/extdata/ismara/targets/FOXP3.p2.txt

inst/extdata/ismara/targets/FOXQ1.p2.txt

inst/extdata/ismara/targets/FOX{C1,C2}.p2.txt

inst/extdata/ismara/targets/FOX{D1,D2}.p2.txt

inst/extdata/ismara/targets/FOX{F1,F2,J1}.p2.txt

inst/extdata/ismara/targets/FOX{I1,J2}.p2.txt

inst/extdata/ismara/targets/GAGAACU.txt

inst/extdata/ismara/targets/GAGAUGA.txt

inst/extdata/ismara/targets/GAGGUAG.txt

inst/extdata/ismara/targets/GATA1..3.p2.txt

inst/extdata/ismara/targets/GATA6.p2.txt

inst/extdata/ismara/targets/GAUAUGU.txt

inst/extdata/ismara/targets/GAUCAGA.txt

inst/extdata/ismara/targets/GAUUGUC.txt

inst/extdata/ismara/targets/GCAGCAU.txt

inst/extdata/ismara/targets/GCUACAU.txt

inst/extdata/ismara/targets/GCUGGUG.txt

inst/extdata/ismara/targets/GFI1.p2.txt

inst/extdata/ismara/targets/GFI1B.p2.txt

inst/extdata/ismara/targets/GGAAGAC.txt

inst/extdata/ismara/targets/GGAAUGU.txt

inst/extdata/ismara/targets/GGACGGA.txt

inst/extdata/ismara/targets/GGAGUGU.txt

inst/extdata/ismara/targets/GGCAAGA.txt

inst/extdata/ismara/targets/GGCAGUG.txt

inst/extdata/ismara/targets/GGCUCAG.txt

inst/extdata/ismara/targets/GLI1..3.p2.txt

inst/extdata/ismara/targets/GTF2A1,2.p2.txt

inst/extdata/ismara/targets/GTF2I.p2.txt

inst/extdata/ismara/targets/GUAAACA.txt

inst/extdata/ismara/targets/GUAACAG.txt

inst/extdata/ismara/targets/GUAGUGU.txt

inst/extdata/ismara/targets/GUCAGUU.txt

inst/extdata/ismara/targets/GUGCAAA.txt

inst/extdata/ismara/targets/GZF1.p2.txt

inst/extdata/ismara/targets/HAND1,2.p2.txt

inst/extdata/ismara/targets/HBP1_HMGB_SSRP1_UBTF.p2.txt

inst/extdata/ismara/targets/HES1.p2.txt

inst/extdata/ismara/targets/HIC1.p2.txt

inst/extdata/ismara/targets/HIF1A.p2.txt

inst/extdata/ismara/targets/HLF.p2.txt

inst/extdata/ismara/targets/HMGA1,2.p2.txt

inst/extdata/ismara/targets/HMX1.p2.txt

inst/extdata/ismara/targets/HNF1A.p2.txt

inst/extdata/ismara/targets/HNF4A_NR2F1,2.p2.txt

inst/extdata/ismara/targets/HOXA9_MEIS1.p2.txt

inst/extdata/ismara/targets/HOX{A4,D4}.p2.txt

inst/extdata/ismara/targets/HOX{A5,B5}.p2.txt

inst/extdata/ismara/targets/HOX{A6,A7,B6,B7}.p2.txt

inst/extdata/ismara/targets/HSF1,2.p2.txt

inst/extdata/ismara/targets/IKZF1.p2.txt

inst/extdata/ismara/targets/IKZF2.p2.txt

inst/extdata/ismara/targets/IRF1,2,7.p3.txt

inst/extdata/ismara/targets/JUN.p2.txt

inst/extdata/ismara/targets/KLF12.p2.txt

inst/extdata/ismara/targets/KLF4.p3.txt

inst/extdata/ismara/targets/LEF1_TCF7_TCF7L1,2.p2.txt

inst/extdata/ismara/targets/LHX3,4.p2.txt

inst/extdata/ismara/targets/LMO2.p2.txt

inst/extdata/ismara/targets/MAFB.p2.txt

inst/extdata/ismara/targets/MAZ.p2.txt

inst/extdata/ismara/targets/MEF2{A,B,C,D}.p2.txt

inst/extdata/ismara/targets/MSX1,2.p2.txt

inst/extdata/ismara/targets/MTF1.p2.txt

inst/extdata/ismara/targets/MYB.p2.txt

inst/extdata/ismara/targets/MYBL2.p2.txt

inst/extdata/ismara/targets/MYFfamily.p2.txt

inst/extdata/ismara/targets/MYOD1.p2.txt

inst/extdata/ismara/targets/MZF1.p2.txt

inst/extdata/ismara/targets/NANOG.p2.txt

inst/extdata/ismara/targets/NANOG{mouse}.p2.txt

inst/extdata/ismara/targets/NFATC1..3.p2.txt

inst/extdata/ismara/targets/NFE2.p2.txt

inst/extdata/ismara/targets/NFE2L1.p2.txt

inst/extdata/ismara/targets/NFE2L2.p2.txt

inst/extdata/ismara/targets/NFIL3.p2.txt

inst/extdata/ismara/targets/NFIX.p2.txt

inst/extdata/ismara/targets/NFKB1_REL_RELA.p2.txt

inst/extdata/ismara/targets/NFY{A,B,C}.p2.txt

inst/extdata/ismara/targets/NHLH1,2.p2.txt

inst/extdata/ismara/targets/NKX2-1,4.p2.txt

inst/extdata/ismara/targets/NKX2-2,8.p2.txt

inst/extdata/ismara/targets/NKX2-3_NKX2-5.p2.txt

inst/extdata/ismara/targets/NKX3-1.p2.txt

inst/extdata/ismara/targets/NKX3-2.p2.txt

inst/extdata/ismara/targets/NKX6-1,2.p2.txt

inst/extdata/ismara/targets/NR1H4.p2.txt

inst/extdata/ismara/targets/NR3C1.p2.txt

inst/extdata/ismara/targets/NR4A2.p2.txt

inst/extdata/ismara/targets/NR5A1,2.p2.txt

inst/extdata/ismara/targets/NR6A1.p2.txt

inst/extdata/ismara/targets/NRF1.p2.txt

inst/extdata/ismara/targets/ONECUT1,2.p2.txt

inst/extdata/ismara/targets/PATZ1.p2.txt

inst/extdata/ismara/targets/PAX2.p2.txt

inst/extdata/ismara/targets/PAX3,7.p2.txt

inst/extdata/ismara/targets/PAX4.p2.txt

inst/extdata/ismara/targets/PAX5.p2.txt

inst/extdata/ismara/targets/PAX6.p2.txt

inst/extdata/ismara/targets/PAX8.p2.txt

inst/extdata/ismara/targets/PBX1.p2.txt

inst/extdata/ismara/targets/PDX1.p2.txt

inst/extdata/ismara/targets/PITX1..3.p2.txt

inst/extdata/ismara/targets/POU1F1.p2.txt

inst/extdata/ismara/targets/POU2F1..3.p2.txt

inst/extdata/ismara/targets/POU3F1..4.p2.txt

inst/extdata/ismara/targets/POU5F1.p2.txt

inst/extdata/ismara/targets/POU5F1_SOX2{dimer}.p2.txt

inst/extdata/ismara/targets/POU6F1.p2.txt

inst/extdata/ismara/targets/PPARG.p2.txt

inst/extdata/ismara/targets/PRDM1.p3.txt

inst/extdata/ismara/targets/PRRX1,2.p2.txt

inst/extdata/ismara/targets/RBPJ.p2.txt

inst/extdata/ismara/targets/REST.p3.txt

inst/extdata/ismara/targets/RFX1..5_RFXANK_RFXAP.p2.txt

inst/extdata/ismara/targets/RORA.p2.txt

inst/extdata/ismara/targets/RREB1.p2.txt

inst/extdata/ismara/targets/RUNX1..3.p2.txt

inst/extdata/ismara/targets/RXRA_VDR{dimer}.p2.txt

inst/extdata/ismara/targets/RXRG_dimer.p3.txt

inst/extdata/ismara/targets/RXR{A,B,G}.p2.txt

inst/extdata/ismara/targets/SMAD1..7,9.p2.txt

inst/extdata/ismara/targets/SNAI1..3.p2.txt

inst/extdata/ismara/targets/SOX17.p2.txt

inst/extdata/ismara/targets/SOX2.p2.txt

inst/extdata/ismara/targets/SOX5.p2.txt

inst/extdata/ismara/targets/SOX{8,9,10}.p2.txt

inst/extdata/ismara/targets/SP1.p2.txt

inst/extdata/ismara/targets/SPI1.p2.txt

inst/extdata/ismara/targets/SPIB.p2.txt

inst/extdata/ismara/targets/SPZ1.p2.txt

inst/extdata/ismara/targets/SREBF1,2.p2.txt

inst/extdata/ismara/targets/SRF.p3.txt

inst/extdata/ismara/targets/SRY.p2.txt

inst/extdata/ismara/targets/STAT1,3.p3.txt

inst/extdata/ismara/targets/STAT2,4,6.p2.txt

inst/extdata/ismara/targets/STAT5{A,B}.p2.txt

inst/extdata/ismara/targets/T.p2.txt

inst/extdata/ismara/targets/TAL1_TCF{3,4,12}.p2.txt

inst/extdata/ismara/targets/TBP.p2.txt

inst/extdata/ismara/targets/TBX4,5.p2.txt

inst/extdata/ismara/targets/TCF4_dimer.p2.txt

inst/extdata/ismara/targets/TEAD1.p2.txt

inst/extdata/ismara/targets/TFAP2B.p2.txt

inst/extdata/ismara/targets/TFAP2{A,C}.p2.txt

inst/extdata/ismara/targets/TFAP4.p2.txt

inst/extdata/ismara/targets/TFCP2.p2.txt

inst/extdata/ismara/targets/TFDP1.p2.txt

inst/extdata/ismara/targets/TFEB.p2.txt

inst/extdata/ismara/targets/TGIF1.p2.txt

inst/extdata/ismara/targets/TLX1..3_NFIC{dimer}.p2.txt

inst/extdata/ismara/targets/TLX2.p2.txt

inst/extdata/ismara/targets/TP53.p2.txt

inst/extdata/ismara/targets/UAAGACG.txt

inst/extdata/ismara/targets/UAAGACU.txt

inst/extdata/ismara/targets/UAAUGCU.txt

inst/extdata/ismara/targets/UAUUGCU.txt

inst/extdata/ismara/targets/UCAAGUA.txt

inst/extdata/ismara/targets/UCACAGU.txt

inst/extdata/ismara/targets/UCACAUU.txt

inst/extdata/ismara/targets/UCCAGUU.txt

inst/extdata/ismara/targets/UCCCUUU.txt

inst/extdata/ismara/targets/UGAAAUG.txt

inst/extdata/ismara/targets/UGACCUA.txt

inst/extdata/ismara/targets/UGCAUAG.txt

inst/extdata/ismara/targets/UGCAUUG.txt

inst/extdata/ismara/targets/UGUGCGU.txt

inst/extdata/ismara/targets/UGUGCUU.txt

inst/extdata/ismara/targets/UUGGCAA.txt

inst/extdata/ismara/targets/UUGGCAC.txt

inst/extdata/ismara/targets/UUGGUCC.txt

inst/extdata/ismara/targets/UUGUUCG.txt

inst/extdata/ismara/targets/UUUUUGC.txt

inst/extdata/ismara/targets/VSX1,2.p2.txt

inst/extdata/ismara/targets/XBP1.p3.txt

inst/extdata/ismara/targets/YY1.p2.txt

inst/extdata/ismara/targets/ZBTB16.p2.txt

inst/extdata/ismara/targets/ZBTB6.p2.txt

inst/extdata/ismara/targets/ZEB1.p2.txt

inst/extdata/ismara/targets/ZFP161.p2.txt

inst/extdata/ismara/targets/ZIC1..3.p2.txt

inst/extdata/ismara/targets/ZNF143.p2.txt

inst/extdata/ismara/targets/ZNF148.p2.txt

inst/extdata/ismara/targets/ZNF238.p2.txt

inst/extdata/ismara/targets/ZNF384.p2.txt

inst/extdata/ismara/targets/ZNF423.p2.txt

inst/extdata/ismara/targets/bHLH_family.p2.txt

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wikiselev/rnaseq.mcf10a
Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

Files in wikiselev/rnaseq.mcf10a
Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

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wikiselev/rnaseq.mcf10a Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

Files in wikiselev/rnaseq.mcf10a Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

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wikiselev/rnaseq.mcf10a
Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"

Files in wikiselev/rnaseq.mcf10a
Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"