.gitignore
LICENSE.rst
README.md
setup.cfg
setup.py
docs/Makefile
docs/make.bat
docs/modules.rst
docs/source/conf.py
docs/source/index.rst
docs/source/release.rst
docs/source/scripts.rst
docs/source/trxtools.rst
docs/source/_static/custom.css
scripts/SAM2profilesGenomic.py
scripts/SAM2profilesTranscripts.py
scripts/csv2pickle.py
scripts/fasta2slidingWindows.py
scripts/genome2WindowsGTF.py
scripts/genomeNascentFolding.py
scripts/mergeSalmon.py
scripts/polyAfraction.py
tests/pseudo_alignment.bam
tests/pseudo_alignment.bam.bai
tests/pseudo_alignment.sam
tests/pseudo_alignment_PROFILE_3end_fwd.bw
tests/pseudo_alignment_PROFILE_3end_polyA_fwd.bw
tests/pseudo_alignment_PROFILE_3end_polyA_rev.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm3-30_fwd.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm3-30_rev.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm5-10_fwd.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm5-10_rev.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm5-30_fwd.bw
tests/pseudo_alignment_PROFILE_3end_polyAmm5-30_rev.bw
tests/pseudo_alignment_PROFILE_3end_rev.bw
tests/pseudo_alignment_PROFILE_5end_fwd.bw
tests/pseudo_alignment_PROFILE_5end_rev.bw
tests/pseudo_alignment_PROFILE_del0_fwd.bw
tests/pseudo_alignment_PROFILE_del0_rev.bw
tests/pseudo_alignment_PROFILE_del3_fwd.bw
tests/pseudo_alignment_PROFILE_del3_rev.bw
tests/pseudo_alignment_PROFILE_read_fwd.bw
tests/pseudo_alignment_PROFILE_read_rev.bw
tests/ref.fasta
tests/ref.fasta.fai
tests/ref.tab
trxtools/BigWig.py
trxtools/__init__.py
trxtools/assays.py
trxtools/go_enrichment.py
trxtools/metaprofiles.py
trxtools/methods.py
trxtools/nascent.py
trxtools/plotting.py
trxtools/profiles.py
trxtools/secondary.py
trxtools.egg-info/PKG-INFO
trxtools.egg-info/SOURCES.txt
trxtools.egg-info/dependency_links.txt
trxtools.egg-info/requires.txt
trxtools.egg-info/top_level.txt
trxtools/sam/SAMgeneral.py
trxtools/sam/SAMgenome.py
trxtools/sam/SAMtranscripts.py
trxtools/sam/__init__.py