Package - cnvkit

Primary informations

Download package: http://deb.debian.org/debian/pool/main/c/cnvkit/cnvkit_0.9.12-1_all.deb (Size: 18.9MiB)

Property	Value
Package	cnvkit
Version	0.9.12-1
Installed-Size	94677
Maintainer	Debian Med Packaging Team
Architecture	all
Depends	python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate (>= 0.15), python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy
Description	Copy number variant detection from targeted DNA sequencing
Description-md5	0b8ab5ba6be9de3379277ab7a92a7b5d
Homepage	https://cnvkit.readthedocs.org
Section	science
Priority	optional
Filename	pool/main/c/cnvkit/cnvkit_0.9.12-1_all.deb
Size	19867944
MD5sum	1bab2eed9e247c45124199c37a680e14
SHA256	ae91c2bce847494e0e295aad3888522f2575eef877bd24355d13ac8236ceac8a

Files in package

• /usr/bin/cnv_annotate.py
• /usr/bin/cnv_expression_correlate.py
• /usr/bin/cnv_updater.py
• /usr/bin/cnvkit.py
• /usr/bin/genome_instability_index.py
• /usr/bin/guess_baits.py
• /usr/bin/reference2targets.py
• /usr/bin/skg_convert.py
• /usr/bin/snpfilter.sh
• /usr/lib/python3/dist-packages/CNVkit-0.9.12.dist-info/INSTALLER
• /usr/lib/python3/dist-packages/CNVkit-0.9.12.dist-info/METADATA
• /usr/lib/python3/dist-packages/CNVkit-0.9.12.dist-info/WHEEL
• /usr/lib/python3/dist-packages/CNVkit-0.9.12.dist-info/entry_points.txt
• /usr/lib/python3/dist-packages/CNVkit-0.9.12.dist-info/top_level.txt
• /usr/lib/python3/dist-packages/cnvlib/__init__.py
• /usr/lib/python3/dist-packages/cnvlib/_version.py
• /usr/lib/python3/dist-packages/cnvlib/access.py
• /usr/lib/python3/dist-packages/cnvlib/antitarget.py
• /usr/lib/python3/dist-packages/cnvlib/autobin.py
• /usr/lib/python3/dist-packages/cnvlib/batch.py
• /usr/lib/python3/dist-packages/cnvlib/bintest.py
• /usr/lib/python3/dist-packages/cnvlib/call.py
• /usr/lib/python3/dist-packages/cnvlib/cluster.py
• /usr/lib/python3/dist-packages/cnvlib/cmdutil.py
• /usr/lib/python3/dist-packages/cnvlib/cnary.py
• /usr/lib/python3/dist-packages/cnvlib/cnvkit.py
• /usr/lib/python3/dist-packages/cnvlib/commands.py
• /usr/lib/python3/dist-packages/cnvlib/core.py
• /usr/lib/python3/dist-packages/cnvlib/coverage.py
• /usr/lib/python3/dist-packages/cnvlib/descriptives.py
• /usr/lib/python3/dist-packages/cnvlib/diagram.py
• /usr/lib/python3/dist-packages/cnvlib/export.py
• /usr/lib/python3/dist-packages/cnvlib/fix.py
• /usr/lib/python3/dist-packages/cnvlib/heatmap.py
• /usr/lib/python3/dist-packages/cnvlib/import_rna.py
• /usr/lib/python3/dist-packages/cnvlib/importers.py
• /usr/lib/python3/dist-packages/cnvlib/metrics.py
• /usr/lib/python3/dist-packages/cnvlib/parallel.py
• /usr/lib/python3/dist-packages/cnvlib/params.py
• /usr/lib/python3/dist-packages/cnvlib/plots.py
• /usr/lib/python3/dist-packages/cnvlib/reference.py
• /usr/lib/python3/dist-packages/cnvlib/reports.py
• /usr/lib/python3/dist-packages/cnvlib/rna.py
• /usr/lib/python3/dist-packages/cnvlib/samutil.py
• /usr/lib/python3/dist-packages/cnvlib/scatter.py
• /usr/lib/python3/dist-packages/cnvlib/segfilters.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/__init__.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/cbs.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/flasso.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/haar.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/hmm.py
• /usr/lib/python3/dist-packages/cnvlib/segmentation/none.py
• /usr/lib/python3/dist-packages/cnvlib/segmetrics.py
• /usr/lib/python3/dist-packages/cnvlib/smoothing.py
• /usr/lib/python3/dist-packages/cnvlib/target.py
• /usr/lib/python3/dist-packages/cnvlib/vary.py
• /usr/lib/python3/dist-packages/skgenome/__init__.py
• /usr/lib/python3/dist-packages/skgenome/chromsort.py
• /usr/lib/python3/dist-packages/skgenome/combiners.py
• /usr/lib/python3/dist-packages/skgenome/gary.py
• /usr/lib/python3/dist-packages/skgenome/intersect.py
• /usr/lib/python3/dist-packages/skgenome/merge.py
• /usr/lib/python3/dist-packages/skgenome/rangelabel.py
• /usr/lib/python3/dist-packages/skgenome/subdivide.py
• /usr/lib/python3/dist-packages/skgenome/subtract.py
• /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py
• /usr/lib/python3/dist-packages/skgenome/tabio/bedio.py
• /usr/lib/python3/dist-packages/skgenome/tabio/genepred.py
• /usr/lib/python3/dist-packages/skgenome/tabio/gff.py
• /usr/lib/python3/dist-packages/skgenome/tabio/picard.py
• /usr/lib/python3/dist-packages/skgenome/tabio/seg.py
• /usr/lib/python3/dist-packages/skgenome/tabio/seqdict.py
• /usr/lib/python3/dist-packages/skgenome/tabio/tab.py
• /usr/lib/python3/dist-packages/skgenome/tabio/textcoord.py
• /usr/lib/python3/dist-packages/skgenome/tabio/util.py
• /usr/lib/python3/dist-packages/skgenome/tabio/vcfio.py
• /usr/lib/python3/dist-packages/skgenome/tabio/vcfsimple.py
• /usr/share/doc/cnvkit/NEWS.Debian.gz
• /usr/share/doc/cnvkit/changelog.Debian.gz
• /usr/share/doc/cnvkit/copyright
• /usr/share/doc/cnvkit/examples/data/access-10kb.hg19.bed
• /usr/share/doc/cnvkit/examples/data/access-10kb.hg38.bed
• /usr/share/doc/cnvkit/examples/data/access-5k-mappable.grch37.bed
• /usr/share/doc/cnvkit/examples/data/access-5k-mappable.hg19.bed
• /usr/share/doc/cnvkit/examples/data/ensembl-gene-info.hg38.tsv
• /usr/share/doc/cnvkit/examples/data/interval-exome.antitarget-9-90kb.bed
• /usr/share/doc/cnvkit/examples/data/interval-exome.target-267.bed
• /usr/share/doc/cnvkit/examples/data/interval-nv2.antitarget-15-150kb.bed
• /usr/share/doc/cnvkit/examples/data/interval-nv2.target-267.bed
• /usr/share/doc/cnvkit/examples/data/refFlat_hg38.txt
• /usr/share/doc/cnvkit/examples/data/tcga-skcm.cnv-expr-corr.tsv
• /usr/share/doc/cnvkit/examples/test/.coveragerc
• /usr/share/doc/cnvkit/examples/test/Makefile
• /usr/share/doc/cnvkit/examples/test/bintest.makefile
• /usr/share/doc/cnvkit/examples/test/clustering.makefile
• /usr/share/doc/cnvkit/examples/test/conftest.py
• /usr/share/doc/cnvkit/examples/test/formats/GRCh37_BRAF.gff.gz
• /usr/share/doc/cnvkit/examples/test/formats/acgh-log10.seg
• /usr/share/doc/cnvkit/examples/test/formats/agilent.bed
• /usr/share/doc/cnvkit/examples/test/formats/amplicon.bed
• /usr/share/doc/cnvkit/examples/test/formats/amplicon.cnr
• /usr/share/doc/cnvkit/examples/test/formats/amplicon.cns
• /usr/share/doc/cnvkit/examples/test/formats/amplicon.text
• /usr/share/doc/cnvkit/examples/test/formats/baits-funky.bed
• /usr/share/doc/cnvkit/examples/test/formats/blank.vcf
• /usr/share/doc/cnvkit/examples/test/formats/chrM-Y-trunc.hg19.fa
• /usr/share/doc/cnvkit/examples/test/formats/cl_seq.cns
• /usr/share/doc/cnvkit/examples/test/formats/cw-tr-log2.seg
• /usr/share/doc/cnvkit/examples/test/formats/dac-my.bed
• /usr/share/doc/cnvkit/examples/test/formats/empty
• /usr/share/doc/cnvkit/examples/test/formats/example.gff
• /usr/share/doc/cnvkit/examples/test/formats/f-on-f.cns
• /usr/share/doc/cnvkit/examples/test/formats/f-on-m.cns
• /usr/share/doc/cnvkit/examples/test/formats/female01.antitargetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/female01.targetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/female02.antitargetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/female02.targetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/gatk-emptyalt.vcf
• /usr/share/doc/cnvkit/examples/test/formats/m-on-f.cns
• /usr/share/doc/cnvkit/examples/test/formats/m-on-m.cns
• /usr/share/doc/cnvkit/examples/test/formats/male01.antitargetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/male01.targetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/male02.antitargetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/male02.targetcoverage.cnn
• /usr/share/doc/cnvkit/examples/test/formats/my-refflat.bed
• /usr/share/doc/cnvkit/examples/test/formats/my-targets.bed
• /usr/share/doc/cnvkit/examples/test/formats/na12878-chrM-Y-trunc.bam
• /usr/share/doc/cnvkit/examples/test/formats/na12878_na12882_mix.vcf
• /usr/share/doc/cnvkit/examples/test/formats/nosample.vcf
• /usr/share/doc/cnvkit/examples/test/formats/nv2_baits.interval_list
• /usr/share/doc/cnvkit/examples/test/formats/nv3.cns
• /usr/share/doc/cnvkit/examples/test/formats/nv3.n3.results
• /usr/share/doc/cnvkit/examples/test/formats/p2-20_1.cnr
• /usr/share/doc/cnvkit/examples/test/formats/p2-20_2.cnr
• /usr/share/doc/cnvkit/examples/test/formats/par-reference.grch38.cnn
• /usr/share/doc/cnvkit/examples/test/formats/ref_test_female.cnn
• /usr/share/doc/cnvkit/examples/test/formats/ref_test_male.cnn
• /usr/share/doc/cnvkit/examples/test/formats/reference-tr.cnn
• /usr/share/doc/cnvkit/examples/test/formats/refflat-mini.txt
• /usr/share/doc/cnvkit/examples/test/formats/tr95t.cns
• /usr/share/doc/cnvkit/examples/test/formats/tr95t.segmetrics.cns
• /usr/share/doc/cnvkit/examples/test/formats/warning.seg
• /usr/share/doc/cnvkit/examples/test/formats/wgs-chr17.cnr
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_1.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_1.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_2.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_2.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_3.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_3.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_4.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_4.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_5.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p1-21_5.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_1.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_1.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_2.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_2.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_3.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_3.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_4.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_4.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_5.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-20_5.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_1.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_1.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_2.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_2.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_5.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-5_5.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_1.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_1.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_2.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_2.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_5.antitargetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/picard/p2-9_5.targetcoverage.csv
• /usr/share/doc/cnvkit/examples/test/regions.bed
• /usr/share/doc/cnvkit/examples/test/test_cnvlib.py
• /usr/share/doc/cnvkit/examples/test/test_commands.py
• /usr/share/doc/cnvkit/examples/test/test_genome.py
• /usr/share/doc/cnvkit/examples/test/test_io.py
• /usr/share/doc/cnvkit/examples/test/test_r.py
• /usr/share/lintian/overrides/cnvkit
• /usr/share/man/man1/cnvkit-access.1.gz
• /usr/share/man/man1/cnvkit-antitarget.1.gz
• /usr/share/man/man1/cnvkit-autobin.1.gz
• /usr/share/man/man1/cnvkit-batch.1.gz
• /usr/share/man/man1/cnvkit-bintest.1.gz
• /usr/share/man/man1/cnvkit-breaks.1.gz
• /usr/share/man/man1/cnvkit-call.1.gz
• /usr/share/man/man1/cnvkit-coverage.1.gz
• /usr/share/man/man1/cnvkit-diagram.1.gz
• /usr/share/man/man1/cnvkit-export.1.gz
• /usr/share/man/man1/cnvkit-fix.1.gz
• /usr/share/man/man1/cnvkit-genemetrics.1.gz
• /usr/share/man/man1/cnvkit-heatmap.1.gz
• /usr/share/man/man1/cnvkit-import-picard.1.gz
• /usr/share/man/man1/cnvkit-import-rna.1.gz
• /usr/share/man/man1/cnvkit-import-seg.1.gz
• /usr/share/man/man1/cnvkit-import-theta.1.gz
• /usr/share/man/man1/cnvkit-metrics.1.gz
• /usr/share/man/man1/cnvkit-reference.1.gz
• /usr/share/man/man1/cnvkit-scatter.1.gz
• /usr/share/man/man1/cnvkit-segment.1.gz
• /usr/share/man/man1/cnvkit-segmetrics.1.gz
• /usr/share/man/man1/cnvkit-sex.1.gz
• /usr/share/man/man1/cnvkit-target.1.gz
• /usr/share/man/py/man1/cnv_annotate.1.gz
• /usr/share/man/py/man1/cnv_expression_correlate.1.gz
• /usr/share/man/py/man1/cnvkit.1.gz