.gitignore
.travis.yml
Dockerfile
LICENSE
MANIFEST.in
README.md
environment.yml
requirements.txt
setup.py
.settings/.gitignore
bin/_preamble.py
bin/alleyoop
bin/slamdunk
bin/splash
hooks/build
slamdunk/__init__.py
slamdunk/alleyoop.py
slamdunk/slamdunk.py
slamdunk/splash.py
slamdunk/version.py
slamdunk.egg-info/PKG-INFO
slamdunk.egg-info/SOURCES.txt
slamdunk.egg-info/dependency_links.txt
slamdunk.egg-info/entry_points.txt
slamdunk.egg-info/requires.txt
slamdunk.egg-info/top_level.txt
slamdunk/contrib/RNASeqReadSimulator/README
slamdunk/contrib/RNASeqReadSimulator/demo/genpairedendreads.sh
slamdunk/contrib/RNASeqReadSimulator/demo/gensingleendreads.sh
slamdunk/contrib/RNASeqReadSimulator/demo/genstrandedreads.sh
slamdunk/contrib/RNASeqReadSimulator/demo/input/reference.fa
slamdunk/contrib/RNASeqReadSimulator/demo/input/sample.bed
slamdunk/contrib/RNASeqReadSimulator/demo/input/sampleposbias.txt
slamdunk/contrib/RNASeqReadSimulator/demo/input/samplereaderror.txt
slamdunk/contrib/RNASeqReadSimulator/src/addvariation2splicingbed.py
slamdunk/contrib/RNASeqReadSimulator/src/genexplvprofile.py
slamdunk/contrib/RNASeqReadSimulator/src/gensimreads.py
slamdunk/contrib/RNASeqReadSimulator/src/getSegs.py
slamdunk/contrib/RNASeqReadSimulator/src/getSegs.pyc
slamdunk/contrib/RNASeqReadSimulator/src/getseqfrombed.py
slamdunk/contrib/RNASeqReadSimulator/src/splitfasta.py
slamdunk/dunks/__init__.py
slamdunk/dunks/deduplicator.py
slamdunk/dunks/dump.py
slamdunk/dunks/filter.py
slamdunk/dunks/mapper.py
slamdunk/dunks/simulator.py
slamdunk/dunks/snps.py
slamdunk/dunks/stats.py
slamdunk/dunks/tcounter.py
slamdunk/plot/PCAPlotter.R
slamdunk/plot/SNPeval.R
slamdunk/plot/__init__.py
slamdunk/plot/checkLibraries.R
slamdunk/plot/compute_context_TC_rates.R
slamdunk/plot/compute_conversion_rate_mle.R
slamdunk/plot/compute_halflifes.R
slamdunk/plot/compute_overall_rates.R
slamdunk/plot/compute_sample_comparison_statistics.R
slamdunk/plot/conversion_per_read_position.R
slamdunk/plot/eval_conversion_rate_plots.R
slamdunk/plot/eval_halflife_per_gene_plots.R
slamdunk/plot/eval_halflifes_error_plot.R
slamdunk/plot/globalRatePlotter.R
slamdunk/plot/merge_rate_files.R
slamdunk/plot/splash_eval_count_files.R
slamdunk/slamseq/SlamSeqFile.py
slamdunk/slamseq/__init__.py
slamdunk/test/__init__.py
slamdunk/test/test_sample.py
slamdunk/test/test_sample.sh
slamdunk/test/data/actb.bed
slamdunk/test/data/reads.fq
slamdunk/test/data/reads_slamdunk_mapped_filtered_tcount.tsv
slamdunk/test/data/ref.fa
slamdunk/utils/BedReader.py
slamdunk/utils/SNPtools.py
slamdunk/utils/__init__.py
slamdunk/utils/misc.py