cleaning

naumenko-sa · Mar 14, 2019 · ba1fc29 · ba1fc29
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diff --git a/.RData b/.RData
diff --git a/.Rhistory b/.Rhistory
diff --git a/.project b/.project
diff --git a/.pydevproject b/.pydevproject
diff --git a/README.md b/README.md
@@ -97,4 +97,7 @@ A +/- flanking region is considered when annotating the 5' and 3' positions of s
 - crt.gonorazky.naumenko.2018 - human bulk RNA-seq to solve Mendelian cases: clustering, outlier analysis, coverage, plots, splicing analysis
 - crt.nishani2018.R - bulk RNA-seq of cancer stem cell experiment
 - crt.utils.R - common function for RNA-seq analysis
-- crt.tropak2018.R - bulk RNA-seq, clustering, DE in mouse
+- crt.tropak2018.R - bulk RNA-seq, clustering, DE in mouse
+
+# Rescourses
+* http://www.rna-seqblog.com
diff --git a/__pycache__/AddJunctionsToDatabase.cpython-35.pyc b/__pycache__/AddJunctionsToDatabase.cpython-35.pyc
diff --git a/__pycache__/AddJunctionsToDatabase1.cpython-35.pyc b/__pycache__/AddJunctionsToDatabase1.cpython-35.pyc
diff --git a/crt.bcbio.stranded.yaml → config/crt.bcbio.stranded.yaml b/crt.bcbio.stranded.yaml → config/crt.bcbio.stranded.yaml
diff --git a/crt.bcbio.twopass.yaml → config/crt.bcbio.twopass.yaml b/crt.bcbio.twopass.yaml → config/crt.bcbio.twopass.yaml
diff --git a/all-protein-coding-genes-no-patches.list → .../all-protein-coding-genes-no-patches.list b/all-protein-coding-genes-no-patches.list → .../all-protein-coding-genes-no-patches.list
diff --git a/gencode.comprehensive.splice.junctions.txt → ...encode.comprehensive.splice.junctions.txt b/gencode.comprehensive.splice.junctions.txt → ...encode.comprehensive.splice.junctions.txt
diff --git a/gene_lengths.txt → data/gene_lengths.txt b/gene_lengths.txt → data/gene_lengths.txt
diff --git a/genes.bed → data/genes.bed b/genes.bed → data/genes.bed
diff --git a/AddJunctionsToDatabase.py → scripts/AddJunctionsToDatabase.py b/AddJunctionsToDatabase.py → scripts/AddJunctionsToDatabase.py
diff --git a/FilterSpliceJunctions.py → scripts/FilterSpliceJunctions.py b/FilterSpliceJunctions.py → scripts/FilterSpliceJunctions.py
diff --git a/SpliceJunctionDiscovery.py → scripts/SpliceJunctionDiscovery.py b/SpliceJunctionDiscovery.py → scripts/SpliceJunctionDiscovery.py
diff --git a/batch_effects.R → scripts/batch_effects.R b/batch_effects.R → scripts/batch_effects.R
diff --git a/bcbio.rnaseq.fix_issue_2135.sh → scripts/bcbio.rnaseq.fix_issue_2135.sh b/bcbio.rnaseq.fix_issue_2135.sh → scripts/bcbio.rnaseq.fix_issue_2135.sh
diff --git a/crt.bam2junctions.pbs → scripts/crt.bam2junctions.pbs b/crt.bam2junctions.pbs → scripts/crt.bam2junctions.pbs
diff --git a/crt.bcbio.default.yaml → scripts/crt.bcbio.default.yaml b/crt.bcbio.default.yaml → scripts/crt.bcbio.default.yaml
diff --git a/crt.bcbio.mm10.yaml → scripts/crt.bcbio.mm10.yaml b/crt.bcbio.mm10.yaml → scripts/crt.bcbio.mm10.yaml
diff --git a/crt.bcbio.noexpression.yaml → scripts/crt.bcbio.noexpression.yaml b/crt.bcbio.noexpression.yaml → scripts/crt.bcbio.noexpression.yaml
diff --git a/crt.coverage.pbs → scripts/crt.coverage.pbs b/crt.coverage.pbs → scripts/crt.coverage.pbs
diff --git a/crt.coverage.sh → scripts/crt.coverage.sh b/crt.coverage.sh → scripts/crt.coverage.sh
diff --git a/crt.coverage_prepare.sh → scripts/crt.coverage_prepare.sh b/crt.coverage_prepare.sh → scripts/crt.coverage_prepare.sh
diff --git a/crt.expression.outliers.R → scripts/crt.expression.outliers.R b/crt.expression.outliers.R → scripts/crt.expression.outliers.R
diff --git a/crt.feature_counts.sh → scripts/crt.feature_counts.sh b/crt.feature_counts.sh → scripts/crt.feature_counts.sh
diff --git a/crt.filter_junctions.sh → scripts/crt.filter_junctions.sh b/crt.filter_junctions.sh → scripts/crt.filter_junctions.sh
diff --git a/crt.gonorazky.naumenko.2018.R → scripts/crt.gonorazky.naumenko.2018.R b/crt.gonorazky.naumenko.2018.R → scripts/crt.gonorazky.naumenko.2018.R
diff --git a/crt.gtex_junctions.R → scripts/crt.gtex_junctions.R b/crt.gtex_junctions.R → scripts/crt.gtex_junctions.R
diff --git a/crt.gtex_junctions.pbs → scripts/crt.gtex_junctions.pbs b/crt.gtex_junctions.pbs → scripts/crt.gtex_junctions.pbs
diff --git a/crt.imbalance.R → scripts/crt.imbalance.R b/crt.imbalance.R → scripts/crt.imbalance.R
diff --git a/crt.imbalance.get_hets.sh → scripts/crt.imbalance.get_hets.sh b/crt.imbalance.get_hets.sh → scripts/crt.imbalance.get_hets.sh
diff --git a/crt.junction_stat.sh → scripts/crt.junction_stat.sh b/crt.junction_stat.sh → scripts/crt.junction_stat.sh
diff --git a/crt.load_junctions.localhd.pbs → scripts/crt.load_junctions.localhd.pbs b/crt.load_junctions.localhd.pbs → scripts/crt.load_junctions.localhd.pbs
diff --git a/crt.load_junctions.pbs → scripts/crt.load_junctions.pbs b/crt.load_junctions.pbs → scripts/crt.load_junctions.pbs
diff --git a/crt.load_junctions.submit.sh → scripts/crt.load_junctions.submit.sh b/crt.load_junctions.submit.sh → scripts/crt.load_junctions.submit.sh
diff --git a/crt.malignant_hypertherimia.R → scripts/crt.malignant_hypertherimia.R b/crt.malignant_hypertherimia.R → scripts/crt.malignant_hypertherimia.R
diff --git a/crt.mds.R → scripts/crt.mds.R b/crt.mds.R → scripts/crt.mds.R
diff --git a/crt.mds.pbs → scripts/crt.mds.pbs b/crt.mds.pbs → scripts/crt.mds.pbs
diff --git a/crt.nishani2018.R → scripts/crt.nishani2018.R b/crt.nishani2018.R → scripts/crt.nishani2018.R
diff --git a/crt.patricia2019.R → scripts/crt.patricia2019.R b/crt.patricia2019.R → scripts/crt.patricia2019.R
diff --git a/crt.prepare4cre.sh → scripts/crt.prepare4cre.sh b/crt.prepare4cre.sh → scripts/crt.prepare4cre.sh
diff --git a/crt.prepare_bcbio_run.sh → scripts/crt.prepare_bcbio_run.sh b/crt.prepare_bcbio_run.sh → scripts/crt.prepare_bcbio_run.sh
diff --git a/crt.qorts.get_novel_exons.sh → scripts/crt.qorts.get_novel_exons.sh b/crt.qorts.get_novel_exons.sh → scripts/crt.qorts.get_novel_exons.sh
diff --git a/crt.remove_low_complexity_reads.sh → scripts/crt.remove_low_complexity_reads.sh b/crt.remove_low_complexity_reads.sh → scripts/crt.remove_low_complexity_reads.sh
diff --git a/crt.splice_junction_summary.pbs → scripts/crt.splice_junction_summary.pbs b/crt.splice_junction_summary.pbs → scripts/crt.splice_junction_summary.pbs
diff --git a/crt.splicing_analysis.pbs → scripts/crt.splicing_analysis.pbs b/crt.splicing_analysis.pbs → scripts/crt.splicing_analysis.pbs
diff --git a/crt.star.index.sh → scripts/crt.star.index.sh b/crt.star.index.sh → scripts/crt.star.index.sh
diff --git a/crt.star.mm10.sh → scripts/crt.star.mm10.sh b/crt.star.mm10.sh → scripts/crt.star.mm10.sh
diff --git a/crt.star.sh → scripts/crt.star.sh b/crt.star.sh → scripts/crt.star.sh
diff --git a/crt.trash.R → scripts/crt.trash.R b/crt.trash.R → scripts/crt.trash.R
diff --git a/crt.tropak2018.R → scripts/crt.tropak2018.R b/crt.tropak2018.R → scripts/crt.tropak2018.R
diff --git a/crt.utils.R → scripts/crt.utils.R b/crt.utils.R → scripts/crt.utils.R
diff --git a/crt.validate.sh → scripts/crt.validate.sh b/crt.validate.sh → scripts/crt.validate.sh
diff --git a/crt.variants.filter.py → scripts/crt.variants.filter.py b/crt.variants.filter.py → scripts/crt.variants.filter.py
diff --git a/crt.variants.trios.sh → scripts/crt.variants.trios.sh b/crt.variants.trios.sh → scripts/crt.variants.trios.sh
diff --git a/crt.yuki2019.R → scripts/crt.yuki2019.R b/crt.yuki2019.R → scripts/crt.yuki2019.R
diff --git a/kremer.2017.R → scripts/kremer.2017.R b/kremer.2017.R → scripts/kremer.2017.R
diff --git a/prinseq-lite.pl → scripts/prinseq-lite.pl b/prinseq-lite.pl → scripts/prinseq-lite.pl