Everyday scripts and analyses

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

Name		Name	Last commit message	Last commit date
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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