Commit a7cdbd7f authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.5.4+dfsg

parent ea77685d

MANIFEST.in

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include pysplicing/include/*

include pysplicing/src/f2c/*

include pysplicing/src/lapack/*

include misopy/settings/*

include misopy/sashimi_plot/settings/*

include misopy/sashimi_plot/test-data/*

include misopy/sashimi_plot/test-data/bam-data/*

include misopy/sashimi_plot/test-data/miso-data/*

include misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/*

include misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/*

include misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/*

include misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/*

include misopy/gff-events/mm9/*

include misopy/gff-events/mm9/genes/*

include misopy/test-data/sam-data/*

include misopy/test-data/se-counts/*
 
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PKG-INFO

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Metadata-Version: 1.1

Name: misopy

Version: 0.5.3

Version: 0.5.4

Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq

Home-page: http://genes.mit.edu/burgelab/miso/

Author: Yarden Katz

misopy.egg-info/PKG-INFO

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Metadata-Version: 1.1

Name: misopy

Version: 0.5.4

Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq

Home-page: http://genes.mit.edu/burgelab/miso/

Author: Yarden Katz

Author-email: yarden@mit.edu

License: UNKNOWN

Description: MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

        

        MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates. 

        

        Please see http://genes.mit.edu/burgelab/miso/docs/ for MISO manual and documentation.

        

Keywords: bioinformatics,sequence analysis,alternative splicing,RNA-Seq,probabilistic models,bayesian

Platform: ALL

Classifier: Development Status :: 4 - Beta

Classifier: Intended Audience :: Science/Research

Classifier: Programming Language :: C

Classifier: Programming Language :: Python

Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

misopy.egg-info/SOURCES.txt

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MANIFEST.in

README

setup.py

misopy/Gene.py

misopy/__init__.py

misopy/as_events.py

misopy/cluster_utils.py

misopy/compare_miso.py

misopy/credible_intervals.py

misopy/exon_utils.py

misopy/filter_events.py

misopy/gff_utils.py

misopy/hypothesis_test.py

misopy/index_gff.py

misopy/json_utils.py

misopy/kde_subclass.py

misopy/legacy_test_pysplicing.py

misopy/misc_utils.py

misopy/miso.py

misopy/miso_db.py

misopy/miso_pack.py

misopy/miso_sampler.py

misopy/miso_utils.py

misopy/miso_zip.py

misopy/module_availability.py

misopy/parse_csv.py

misopy/parse_gene.py

misopy/pe_utils.py

misopy/pickle_utils.py

misopy/py2c_gene.py

misopy/read_simulator.py

misopy/reads_utils.py

misopy/run_events_analysis.py

misopy/run_miso.py

misopy/sam_rpkm.py

misopy/sam_to_bam.py

misopy/sam_utils.py

misopy/samples_utils.py

misopy/settings.py

misopy/summarize_miso.py

misopy/test_cluster.py

misopy/test_miso.py

misopy.egg-info/PKG-INFO

misopy.egg-info/SOURCES.txt

misopy.egg-info/dependency_links.txt

misopy.egg-info/entry_points.txt

misopy.egg-info/pbr.json

misopy.egg-info/requires.txt

misopy.egg-info/top_level.txt

misopy/gff-events/mm9/SE.mm9.gff

misopy/gff-events/mm9/genes/Atp2b1.mm9.gff

misopy/sashimi_plot/Sashimi.py

misopy/sashimi_plot/__init__.py

misopy/sashimi_plot/plot.py

misopy/sashimi_plot/sashimi_plot.py

misopy/sashimi_plot/plot_utils/__init__.py

misopy/sashimi_plot/plot_utils/plot_gene.py

misopy/sashimi_plot/plot_utils/plot_settings.py

misopy/sashimi_plot/plot_utils/plotting.py

misopy/sashimi_plot/plot_utils/samples_plotter.py

misopy/sashimi_plot/settings/sashimi_plot_settings.txt

misopy/sashimi_plot/test-data/events.gff

misopy/sashimi_plot/test-data/bam-data/heartKOa.bam.bai

misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam

misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam.bai

misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam

misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam.bai

misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam

misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam.bai

misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam

misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam.bai

misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso

misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso

misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso

misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso

misopy/settings/miso_settings.txt

misopy/test-data/sam-data/c2c12.Atp2b1.sam

pysplicing/include/f2c.h

pysplicing/include/matrix.pmt

pysplicing/include/pyerror.h

pysplicing/include/pysplicing.h

pysplicing/include/random.h

pysplicing/include/splicing.h

pysplicing/include/splicing_error.h

pysplicing/include/splicing_lapack.h

pysplicing/include/splicing_matrix.h

pysplicing/include/splicing_matrix_pmt.h

pysplicing/include/splicing_memory.h

pysplicing/include/splicing_pmt.h

pysplicing/include/splicing_pmt_off.h

pysplicing/include/splicing_random.h

pysplicing/include/splicing_vector.h

pysplicing/include/splicing_vector_pmt.h

pysplicing/include/vector.pmt

pysplicing/pysplicing/__init__.py

pysplicing/src/assignment.c

pysplicing/src/blas.c

pysplicing/src/complexity.c

pysplicing/src/convert.c

pysplicing/src/error.c

pysplicing/src/fortran_stuff.c

pysplicing/src/gff.c

pysplicing/src/ident.c

pysplicing/src/lapack.c

pysplicing/src/lawson_hanson_nnls.c

pysplicing/src/matrix.c

pysplicing/src/memory.c

pysplicing/src/miso.c

pysplicing/src/miso_paired.c

pysplicing/src/nnls.c

pysplicing/src/pyconvert.c

pysplicing/src/pyerror.c

pysplicing/src/pyrandom.c

pysplicing/src/pysplicing.c

pysplicing/src/qsort.c

pysplicing/src/qsort_r.c

pysplicing/src/random.c

pysplicing/src/simulator.c

pysplicing/src/solve.c

pysplicing/src/strvector.c

pysplicing/src/util.c

pysplicing/src/vector.c

pysplicing/src/f2c/Notice

pysplicing/src/f2c/README

pysplicing/src/f2c/abort_.c

pysplicing/src/f2c/arith.h

pysplicing/src/f2c/backspac.c

pysplicing/src/f2c/c_abs.c

pysplicing/src/f2c/c_cos.c

pysplicing/src/f2c/c_div.c

pysplicing/src/f2c/c_exp.c

pysplicing/src/f2c/c_log.c

pysplicing/src/f2c/c_sin.c

pysplicing/src/f2c/c_sqrt.c

pysplicing/src/f2c/cabs.c

pysplicing/src/f2c/changes

pysplicing/src/f2c/close.c

pysplicing/src/f2c/comptry.bat

pysplicing/src/f2c/ctype.c

pysplicing/src/f2c/d_abs.c

pysplicing/src/f2c/d_acos.c

pysplicing/src/f2c/d_asin.c

pysplicing/src/f2c/d_atan.c

pysplicing/src/f2c/d_atn2.c

pysplicing/src/f2c/d_cnjg.c

pysplicing/src/f2c/d_cos.c

pysplicing/src/f2c/d_cosh.c

pysplicing/src/f2c/d_dim.c

pysplicing/src/f2c/d_exp.c

pysplicing/src/f2c/d_imag.c

pysplicing/src/f2c/d_int.c

pysplicing/src/f2c/d_lg10.c

pysplicing/src/f2c/d_log.c

pysplicing/src/f2c/d_mod.c

pysplicing/src/f2c/d_nint.c

pysplicing/src/f2c/d_prod.c

pysplicing/src/f2c/d_sin.c

pysplicing/src/f2c/d_sinh.c

pysplicing/src/f2c/d_sqrt.c

pysplicing/src/f2c/d_tan.c

pysplicing/src/f2c/d_tanh.c

pysplicing/src/f2c/derf_.c

pysplicing/src/f2c/derfc_.c

pysplicing/src/f2c/dfe.c

pysplicing/src/f2c/dolio.c

pysplicing/src/f2c/dtime_.c

pysplicing/src/f2c/due.c

pysplicing/src/f2c/dummy.c

pysplicing/src/f2c/ef1asc_.c

pysplicing/src/f2c/ef1cmc_.c

pysplicing/src/f2c/endfile.c

pysplicing/src/f2c/erf_.c

pysplicing/src/f2c/erfc_.c

pysplicing/src/f2c/err.c

pysplicing/src/f2c/etime_.c

pysplicing/src/f2c/exit_.c

pysplicing/src/f2c/f2c.h

pysplicing/src/f2c/f2c.h0

pysplicing/src/f2c/f2ch.add

pysplicing/src/f2c/f77_aloc.c

pysplicing/src/f2c/f77vers.c

pysplicing/src/f2c/fctype.h

pysplicing/src/f2c/fio.h

pysplicing/src/f2c/fmt.c

pysplicing/src/f2c/fmt.h

pysplicing/src/f2c/fmtlib.c

pysplicing/src/f2c/fp.h

pysplicing/src/f2c/ftell_.c

pysplicing/src/f2c/getarg_.c

pysplicing/src/f2c/getenv_.c

pysplicing/src/f2c/h_abs.c

pysplicing/src/f2c/h_dim.c

pysplicing/src/f2c/h_dnnt.c

pysplicing/src/f2c/h_indx.c

pysplicing/src/f2c/h_len.c

pysplicing/src/f2c/h_mod.c

pysplicing/src/f2c/h_nint.c

pysplicing/src/f2c/h_sign.c

pysplicing/src/f2c/hl_ge.c

pysplicing/src/f2c/hl_gt.c

pysplicing/src/f2c/hl_le.c

pysplicing/src/f2c/hl_lt.c

pysplicing/src/f2c/i77vers.c

pysplicing/src/f2c/i_abs.c

pysplicing/src/f2c/i_dim.c

pysplicing/src/f2c/i_dnnt.c

pysplicing/src/f2c/i_indx.c

pysplicing/src/f2c/i_len.c

pysplicing/src/f2c/i_mod.c

pysplicing/src/f2c/i_nint.c

pysplicing/src/f2c/i_sign.c

pysplicing/src/f2c/iargc_.c

pysplicing/src/f2c/iio.c

pysplicing/src/f2c/ilnw.c

pysplicing/src/f2c/inquire.c

pysplicing/src/f2c/l_ge.c

pysplicing/src/f2c/l_gt.c

pysplicing/src/f2c/l_le.c

pysplicing/src/f2c/l_lt.c

pysplicing/src/f2c/lbitbits.c

pysplicing/src/f2c/lbitshft.c

pysplicing/src/f2c/libf2c.lbc

pysplicing/src/f2c/libf2c.sy

pysplicing/src/f2c/lio.h

pysplicing/src/f2c/lread.c

pysplicing/src/f2c/lwrite.c

pysplicing/src/f2c/main.c

pysplicing/src/f2c/makefile.sy

pysplicing/src/f2c/makefile.u

pysplicing/src/f2c/makefile.vc

pysplicing/src/f2c/makefile.wat

pysplicing/src/f2c/math.hvc

pysplicing/src/f2c/mkfile.plan9

pysplicing/src/f2c/open.c

pysplicing/src/f2c/pow_ci.c

pysplicing/src/f2c/pow_dd.c

pysplicing/src/f2c/pow_di.c

pysplicing/src/f2c/pow_hh.c

pysplicing/src/f2c/pow_ii.c

pysplicing/src/f2c/pow_ri.c

pysplicing/src/f2c/pow_zi.c

pysplicing/src/f2c/pow_zz.c

pysplicing/src/f2c/r_abs.c

pysplicing/src/f2c/r_acos.c

pysplicing/src/f2c/r_asin.c

pysplicing/src/f2c/r_atan.c

pysplicing/src/f2c/r_atn2.c

pysplicing/src/f2c/r_cnjg.c

pysplicing/src/f2c/r_cos.c

pysplicing/src/f2c/r_cosh.c

pysplicing/src/f2c/r_dim.c

pysplicing/src/f2c/r_exp.c

pysplicing/src/f2c/r_imag.c

pysplicing/src/f2c/r_int.c

pysplicing/src/f2c/r_lg10.c

pysplicing/src/f2c/r_log.c

pysplicing/src/f2c/r_mod.c

pysplicing/src/f2c/r_nint.c

pysplicing/src/f2c/r_sign.c

pysplicing/src/f2c/r_sin.c

pysplicing/src/f2c/r_sinh.c

pysplicing/src/f2c/r_sqrt.c

pysplicing/src/f2c/r_tan.c

pysplicing/src/f2c/r_tanh.c

pysplicing/src/f2c/rawio.h

pysplicing/src/f2c/rdfmt.c

pysplicing/src/f2c/rewind.c

pysplicing/src/f2c/rsfe.c

pysplicing/src/f2c/rsli.c

pysplicing/src/f2c/rsne.c

pysplicing/src/f2c/s_cat.c

pysplicing/src/f2c/s_cmp.c

pysplicing/src/f2c/s_copy.c

pysplicing/src/f2c/s_paus.c

pysplicing/src/f2c/s_rnge.c

pysplicing/src/f2c/s_stop.c

pysplicing/src/f2c/scomptry.bat

pysplicing/src/f2c/sfe.c

pysplicing/src/f2c/sig_die.c

pysplicing/src/f2c/signal1.h

pysplicing/src/f2c/signal1.h0

pysplicing/src/f2c/signal_.c

pysplicing/src/f2c/signbit.c

pysplicing/src/f2c/sue.c

pysplicing/src/f2c/sysdep1.h

pysplicing/src/f2c/sysdep1.h0

pysplicing/src/f2c/system_.c

pysplicing/src/f2c/typesize.c

pysplicing/src/f2c/uio.c

pysplicing/src/f2c/uninit.c

pysplicing/src/f2c/util.c

pysplicing/src/f2c/wref.c

pysplicing/src/f2c/wrtfmt.c

pysplicing/src/f2c/wsfe.c

pysplicing/src/f2c/wsle.c

pysplicing/src/f2c/wsne.c

pysplicing/src/f2c/xsum0.out

pysplicing/src/f2c/xwsne.c

pysplicing/src/f2c/z_abs.c

pysplicing/src/f2c/z_cos.c

pysplicing/src/f2c/z_div.c

pysplicing/src/f2c/z_exp.c

pysplicing/src/f2c/z_log.c

pysplicing/src/f2c/z_sin.c

pysplicing/src/f2c/z_sqrt.c

pysplicing/src/lapack/blas.inc

pysplicing/src/lapack/dbdsdc.c

pysplicing/src/lapack/dbdsqr.c

pysplicing/src/lapack/dcopy.c

pysplicing/src/lapack/ddot.c

pysplicing/src/lapack/debug.h

pysplicing/src/lapack/dgebd2.c

pysplicing/src/lapack/dgebrd.c

pysplicing/src/lapack/dgelq2.c

pysplicing/src/lapack/dgelqf.c

pysplicing/src/lapack/dgemm.c

pysplicing/src/lapack/dgemv.c

pysplicing/src/lapack/dgeqr2.c

pysplicing/src/lapack/dgeqrf.c

pysplicing/src/lapack/dger.c

pysplicing/src/lapack/dgesdd.c

pysplicing/src/lapack/disnan.c

pysplicing/src/lapack/dlabrd.c

pysplicing/src/lapack/dlacpy.c

pysplicing/src/lapack/dlaed6.c

pysplicing/src/lapack/dlaisnan.c

pysplicing/src/lapack/dlamch.c

pysplicing/src/lapack/dlamrg.c

pysplicing/src/lapack/dlange.c

pysplicing/src/lapack/dlanst.c

pysplicing/src/lapack/dlapy2.c

pysplicing/src/lapack/dlarf.c

pysplicing/src/lapack/dlarfb.c

pysplicing/src/lapack/dlarfg.c

pysplicing/src/lapack/dlarft.c

pysplicing/src/lapack/dlartg.c

pysplicing/src/lapack/dlas2.c

pysplicing/src/lapack/dlascl.c

pysplicing/src/lapack/dlasd0.c

pysplicing/src/lapack/dlasd1.c

pysplicing/src/lapack/dlasd2.c

pysplicing/src/lapack/dlasd3.c

pysplicing/src/lapack/dlasd4.c

pysplicing/src/lapack/dlasd5.c

pysplicing/src/lapack/dlasd6.c

pysplicing/src/lapack/dlasd7.c

pysplicing/src/lapack/dlasd8.c

pysplicing/src/lapack/dlasda.c

pysplicing/src/lapack/dlasdq.c

pysplicing/src/lapack/dlasdt.c

pysplicing/src/lapack/dlaset.c

pysplicing/src/lapack/dlasq1.c

pysplicing/src/lapack/dlasq2.c

pysplicing/src/lapack/dlasq3.c

pysplicing/src/lapack/dlasq4.c

pysplicing/src/lapack/dlasq5.c

pysplicing/src/lapack/dlasq6.c

pysplicing/src/lapack/dlasr.c

pysplicing/src/lapack/dlasrt.c

pysplicing/src/lapack/dlassq.c

pysplicing/src/lapack/dlasv2.c

pysplicing/src/lapack/dnrm2.c

pysplicing/src/lapack/dorg2r.c

pysplicing/src/lapack/dorgbr.c

pysplicing/src/lapack/dorgl2.c

pysplicing/src/lapack/dorglq.c

pysplicing/src/lapack/dorgqr.c

pysplicing/src/lapack/dorm2r.c

pysplicing/src/lapack/dormbr.c

pysplicing/src/lapack/dorml2.c

pysplicing/src/lapack/dormlq.c

pysplicing/src/lapack/dormqr.c

pysplicing/src/lapack/drot.c

pysplicing/src/lapack/dscal.c

pysplicing/src/lapack/dswap.c

pysplicing/src/lapack/dtrmm.c

pysplicing/src/lapack/dtrmv.c

pysplicing/src/lapack/ieeeck.c

pysplicing/src/lapack/iladlc.c

pysplicing/src/lapack/iladlr.c

pysplicing/src/lapack/ilaenv.c

pysplicing/src/lapack/iparmq.c

pysplicing/src/lapack/lapack.inc

pysplicing/src/lapack/len_trim.c

pysplicing/src/lapack/lsame.c

pysplicing/src/lapack/stat.h

pysplicing/src/lapack/xerbla.c
 
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misopy.egg-info/dependency_links.txt

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