Everyday scripts and analyses

The scripts under this directory have been modified to work with makefiles.

Name		Name	Last commit message	Last commit date
Latest commit History 224 Commits
Rscripts		Rscripts
pyatactools		pyatactools
Hendrich_PolII_mm10.R		Hendrich_PolII_mm10.R
Hendrich_genebased_polII.pl		Hendrich_genebased_polII.pl
README.md		README.md
SPIA_mouse_from_deseq.R		SPIA_mouse_from_deseq.R
TAC-plots.R		TAC-plots.R
alignment.make		alignment.make
annotate-nurd-peaks.R		annotate-nurd-peaks.R
annotate-peak.R		annotate-peak.R
annotate-regions.R		annotate-regions.R
bam-to-bw-strand-specific.sh		bam-to-bw-strand-specific.sh
bam-to-bw.pl		bam-to-bw.pl
bam-to-sam.sh		bam-to-sam.sh
bh-Gene-Ontology.R		bh-Gene-Ontology.R
bh-compare-Epi-ES-peaks.R		bh-compare-Epi-ES-peaks.R
bh-compare-intron-exon-expression.R		bh-compare-intron-exon-expression.R
bh-differential-eRNA-expression.R		bh-differential-eRNA-expression.R
bh-differential-exon.R		bh-differential-exon.R
bh-differential-intron.R		bh-differential-intron.R
bh-fold-change-density.R		bh-fold-change-density.R
bh-make-heatmaps.R		bh-make-heatmaps.R
check-chip-enrichment.pl		check-chip-enrichment.pl
classify-range.R		classify-range.R
compare-macs2-broad-summits.R		compare-macs2-broad-summits.R
compare-profiles.py		compare-profiles.py
compare-regions-mean-signal.R		compare-regions-mean-signal.R
compare-summits-tss.R		compare-summits-tss.R
convert-bed-plus-to-gtf.R		convert-bed-plus-to-gtf.R
convert-chrom-name.pl		convert-chrom-name.pl
convert-ensembl-gtf.sh		convert-ensembl-gtf.sh
convert-npz2csv.py		convert-npz2csv.py
count-bowtie-reads.sh		count-bowtie-reads.sh
count-tags.py		count-tags.py
count-tags.pyc		count-tags.pyc
deBH.R		deBH.R
deBH_new.R		deBH_new.R
differential-binding.R		differential-binding.R
distinct-colors.py		distinct-colors.py
download-sra.bash		download-sra.bash
es2epi-transition.R		es2epi-transition.R
examine-peaks.R		examine-peaks.R
extract-gene-aliases.sh		extract-gene-aliases.sh
extract-sra-info.pl		extract-sra-info.pl
filter-annotation-by-description.R		filter-annotation-by-description.R
genePredToSqlite.pl		genePredToSqlite.pl
get-IDR-threshold.R		get-IDR-threshold.R
get-annotation-rscript.R		get-annotation-rscript.R
get-annotation.R		get-annotation.R
get-average-profile-bins.R		get-average-profile-bins.R
get-average-profile.py		get-average-profile.py
get-common-peaks.R		get-common-peaks.R
get-enhancers.R		get-enhancers.R
get-ensembl-regulation.R		get-ensembl-regulation.R
get-insert-size.sh		get-insert-size.sh
get-motifs.R		get-motifs.R
get-peak-correlation.R		get-peak-correlation.R
get-protocol-strand-interpretation.sh		get-protocol-strand-interpretation.sh
get-se-strand-specific-bigwig.pl		get-se-strand-specific-bigwig.pl
get-travelling-ratio.R		get-travelling-ratio.R
handle-ext-dep.make		handle-ext-dep.make
helpers.make		helpers.make
identify-targets-from-profile.R		identify-targets-from-profile.R
install-pyatactools.sh		install-pyatactools.sh
install-tmux.sh		install-tmux.sh
make-bigwig.sh		make-bigwig.sh
make-expr-density-plot.R		make-expr-density-plot.R
make-intron-bed.sh		make-intron-bed.sh
make-pseudoreps.sh		make-pseudoreps.sh
make-scores-negative.sh		make-scores-negative.sh
make-test-file.R		make-test-file.R
make-tf-over-enhancers.sh		make-tf-over-enhancers.sh
make-trascript-db.R		make-trascript-db.R
matrix-normalisation.make		matrix-normalisation.make
merge-bam.sh		merge-bam.sh
merge-gsnap-halfmapping-concordant.sh		merge-gsnap-halfmapping-concordant.sh
merge-gsnap-pe-njobs.sh		merge-gsnap-pe-njobs.sh
merge-gsnap-se-njobs.sh		merge-gsnap-se-njobs.sh
nurd-prc2-common.R		nurd-prc2-common.R
overlap-multiple-ranges.R		overlap-multiple-ranges.R
pairwise-comb.awk		pairwise-comb.awk
peak-calling.make		peak-calling.make
plot-alignment-stats.R		plot-alignment-stats.R
plot-bw-correlation.R		plot-bw-correlation.R
plot-chip-enrichment.R		plot-chip-enrichment.R
plot-fpkms.R		plot-fpkms.R
plot-metagene.py		plot-metagene.py
plot-profiles.py		plot-profiles.py
polished-plots.R		polished-plots.R
pool-replicates.make		pool-replicates.make
print-make-vars.sh		print-make-vars.sh
pyatactools-dev		pyatactools-dev
quality-control.make		quality-control.make
quality-control.sh		quality-control.sh
read-chip-bams.R		read-chip-bams.R
remove-ranges-from-file.R		remove-ranges-from-file.R
run-ChromHMM.sh		run-ChromHMM.sh
run-IDR.sh		run-IDR.sh
run-bigWigCorrelate-on-pairs.sh		run-bigWigCorrelate-on-pairs.sh
run-bowtie.sh		run-bowtie.sh

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