Tree:
f27ea5443b
11.0
12.0
12.1
12.2
13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
libressl-gopher-test
master
misc-fixes
python-renames
rworkman
urchlay
user/aclemons/updates
user/anddt/development/acpica
user/anddt/development/glm
user/anddt/development/gnustep-base
user/anddt/development/gnustep-make
user/anddt/games/assaultcube-reloaded
user/anddt/games/doomseeker
user/anddt/games/prboom-plus
user/anddt/games/rocksndiamonds
user/anddt/games/rottexpr
user/anddt/games/srb2
user/anddt/graphics/blender
user/anddt/graphics/maim
user/anddt/ham/chirp
user/anddt/ham/hamlib
user/anddt/libraries/girara
user/anddt/libraries/goffice
user/anddt/libraries/gtksourceview4
user/anddt/libraries/imlib2
user/anddt/libraries/jsoncpp
user/anddt/libraries/libnova
user/anddt/libraries/libopenmpt
user/anddt/libraries/libtorrent
user/anddt/libraries/wxGTK3
user/anddt/libraries/xmlrpc-c
user/anddt/misc/discount
user/anddt/misc/slop
user/anddt/network/nethogs
user/anddt/network/putty
user/anddt/network/rclone
user/anddt/network/rtorrent
user/anddt/network/sshguard
user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
user/anddt/system/zzzfm
user/belka/updates
user/chris.willing/updates
user/dslackw/updates
user/elyk/updates
user/kingbeowulf/updates
user/mario/updates
user/ponce/updates
user/pprkut/updates
willysr
wxWidgets-wip
GPG-KEY
15.0-20230325.1
15.0-20230318.1
15.0-20230312.1
15.0-20230304.1
15.0-20230225.1
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15.0-20230204.1
15.0-20230128.1
15.0-20230121.1
15.0-20230114.1
15.0-20230107.1
15.0-20221231.1
15.0-20221223.1
15.0-20221217.1
15.0-20221210.1
15.0-20221203.1
15.0-20221126.1
15.0-20221119.1
15.0-20221112.1
15.0-20221105.1
15.0-20221029.1
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15.0-20220702.1
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15.0-20220604.1
15.0-20220528.1
15.0-20220521.1
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15.0-20220430.1
15.0-20220423.1
15.0-20220416.1
15.0-20220409.1
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15.0-20220326.1
15.0-20220320.1
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14.2-20210417.1
14.2-20210410.1
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14.2-20201003.1
14.2-20200926.1
14.2-20200919.1
14.2-20200912.1
14.2-20200905.1
14.2-20200829.1
14.2-20200628.1
14.2-20200620.1
14.2-20200614.1
14.2-20200606.1
14.2-20200601.1
14.2-20200523.1
14.2-20200516.1
14.2-20200510.1
14.2-20200503.1
14.2-20200424.1
14.2-20200419.1
14.2-20200411.1
14.2-20200406.1
14.2-20200404.1
14.2-20200328.1
14.2-20200321.1
14.2-20200314.1
14.2-20200307.1
14.2-20200229.1
14.2-20200223.1
14.2-20200215.1
14.2-20200208.1
14.2-20200201.1
14.2-20200126.1
14.2-20200118.1
14.2-20200112.1
14.2-20200103.1
14.2-20191231.1
14.2-20191221.1
14.2-20191215.1
14.2-20191207.1
14.2-20191201.1
14.2-20191123.1
14.2-20191116.1
14.2-20191109.1
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14.2-20191026.1
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14.2-20190706.1
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14.2-20190601.1
14.2-20190525.1
14.2-20190518.1
14.2-20190511.1
14.2-20190504.1
14.2-20190427.1
14.2-20190420.1
14.2-20190413.1
14.2-20190406.1
14.2-20190330.1
14.2-20190323.1
14.2-20190316.1
14.2-20190302.1
14.2-20190223.1
14.2-20190217.1
14.2-20190209.1
14.2-20190202.1
14.2-20190126.1
14.2-20190119.1
14.2-20190112.1
14.2-20190105.1
14.2-20181229.1
14.2-20181225.1
14.2-20181222.1
14.2-20181215.1
14.2-20181209.1
14.2-20181201.1
14.2-20181124.1
14.2-20181117.1
14.2-20181110.1
14.2-20181103.1
14.2-20181027.1
14.2-20181020.1
14.2-20181013.1
14.2-20181006.1
14.2-20180929.1
14.2-20180923.1
14.2-20180922.1
14.2-20180915.1
14.2-20180908.1
14.2-20180901.1
14.2-20180825.1
14.2-20180818.1
14.2-20180811.1
14.2-20180804.1
14.2-20180728.1
14.2-20180721.1
14.2-20180717.1
14.2-20180714.1
14.2-20180707.1
14.2-20180630.1
14.2-20180623.1
14.2-20180618.1
14.2-20180614.1
14.2-20180609.1
14.2-20180602.1
14.2-20180526.1
14.2-20180520.1
14.2-20180519.1
14.2-20180512.1
14.2-20180504.1
14.2-20180427.1
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14.2-20180407.1
14.2-20180401.1
14.2-20180331.1
14.2-20180324.1
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14.2-20180310.1
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14.2-20180303.1
14.2-20180224.1
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14.2-20180210.1
14.2-20180203.1
14.2-20180127.1
14.2-20180120.1
14.2-20180117.1
14.2-20180113.1
14.2-20180110.1
14.2-20180106.1
14.2-20171228.1
14.2-20171223.1
14.2-20171221.1
14.2-20171216.1
14.2-20171209.1
14.2-20171201.1
14.2-20171124.1
14.2-20171120.1
14.2-20171118.1
14.2-20171111.1
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14.2-20171101
14.2-20171028.1
14.2-20171021.1
14.2-20171014.2
14.2-20171014.1
14.2-20171010.1
14.2-20171007.1
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14.2-20170902.1
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14.2-20170805.1
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14.2-20170726.1
14.2-20170722.1
14.2-20170715.1
14.2-20170712.1
14.2-20170708.1
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14.2-20170610.1
14.2-20170606.1
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14.2-20170128.1
14.2-20170124.1
14.2-20170121.1
14.2-20170114.1
14.2-20170110.1
14.2-20170109.1
14.2-20170107.1
14.2-20161231.1
14.2-20161224.1
14.2-20161217.2
14.2-20161217.1
14.2-20161210.1
14.2-20161204.1
14.2-20161203.1
14.2-20161126.1
14.2-20161119.1
14.2-20161115.1
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14.2-20161105.1
14.2-20161029.1
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14.2-20161015.1
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14.2-20161001.2
14.2-20161001.1
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14.2-20160914.1
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14.2-20160717.2
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Andrew Clemons
551eaa9aa0
academic/cufflinks: Fix info file.
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2 years ago | |
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| README | cd2507649b academic/cufflinks: use binaries | 3 years ago |
| References | 5094f4b727 academic/cufflinks: Added (reference-guided assembler for RNA-Seq). | 11 years ago |
| cufflinks.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 3 years ago |
| cufflinks.info | 551eaa9aa0 academic/cufflinks: Fix info file. | 2 years ago |
| slack-desc | b4944ef974 academic/cufflinks: Updated for version 2.2.1. | 10 years ago |
README
Cufflinks assembles transcripts, estimates their abundances, and tests
for differential expression and regulation in RNA-Seq samples. It
accepts aligned RNA-Seq reads and assembles the alignments into a
parsimonious set of transcripts. Cufflinks then estimates the relative
abundances of these transcripts based on how many reads support each
one, taking into account biases in library preparation protocols.
Cufflinks is a collaborative effort between the Laboratory for
Mathematical and Computational Biology, led by Lior Pachter at UC
Berkeley, Steven Salzberg's computational genomics group at the
Institute of Genetic Medicine at Johns Hopkins University, and Barbara
Wold's lab at Caltech.
NOTE: This just repackages the binaries provided from upstream.
Reference:
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)
for differential expression and regulation in RNA-Seq samples. It
accepts aligned RNA-Seq reads and assembles the alignments into a
parsimonious set of transcripts. Cufflinks then estimates the relative
abundances of these transcripts based on how many reads support each
one, taking into account biases in library preparation protocols.
Cufflinks is a collaborative effort between the Laboratory for
Mathematical and Computational Biology, led by Lior Pachter at UC
Berkeley, Steven Salzberg's computational genomics group at the
Institute of Genetic Medicine at Johns Hopkins University, and Barbara
Wold's lab at Caltech.
NOTE: This just repackages the binaries provided from upstream.
Reference:
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)