Your message dated Wed, 21 Oct 2015 11:00:18 +0000 with message-id <E1Zor7y-0002yU-89@franck.debian.org> and subject line Bug#778578: fixed in rsem 1.2.22+dfsg-1 has caused the Debian Bug report #778578, regarding ITP: rsem -- RNA-Seq by Expectation-Maximization to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 778578: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778578 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
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- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: rsem -- RNA-Seq by Expectation-Maximization
- From: Michael Crusoe <michael.crusoe@gmail.com>
- Date: Mon, 16 Feb 2015 23:18:44 +0000
- Message-id: <CAD=WrcJkcxU4chT4x1Dc2CmJFbmQaOiii1e2bexMKCJ+ijoybQ@mail.gmail.com>
Package: wnppSeverity: wishlistOwner: Debian Med team <debian-med@lists.debian.org>X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org* Package name : rsemVersion : 1.2.19Upstream Author : Bo Li <bli25 [at] berkeley [dot] edu>* License : GPL-3Programming Lang: C++, PerlDescription : RNA-Seq by Expectation-MaximizationRSEM is a software package for estimating gene and isoform _expression_levels from RNA-Seq data. The RSEM package provides an user-friendlyinterface, supports threads for parallel computation of the EMalgorithm, single-end and paired-end read data, quality scores,variable-length reads and RSPD estimation. In addition, it providesposterior mean and 95% credibility interval estimates for _expression_levels. For visualization, It can generate BAM and Wiggle files in bothtranscript-coordinate and genomic-coordinate. Genomic-coordinate filescan be visualized by both UCSC Genome browser and Broad Institute’sIntegrative Genomics Viewer (IGV). Transcript-coordinate files can bevisualized by IGV. RSEM also has its own scripts to generate transcriptread depth plots in pdf format. The unique feature of RSEM is, the readdepth plots can be stacked, with read depth contributed to unique readsshown in black and contributed to multi-reads shown in red. In addition,models learned from data can also be visualized. Last but not least,RSEM contains a simulator.RSEM is a popular bioinformatics program and a dependency of trinityrnaseq. It will be maintained by the Debian Med team.
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- To: 778578-close@bugs.debian.org
- Subject: Bug#778578: fixed in rsem 1.2.22+dfsg-1
- From: crusoe@ucdavis.edu (Michael R. Crusoe)
- Date: Wed, 21 Oct 2015 11:00:18 +0000
- Message-id: <E1Zor7y-0002yU-89@franck.debian.org>
Source: rsem Source-Version: 1.2.22+dfsg-1 We believe that the bug you reported is fixed in the latest version of rsem, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 778578@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <crusoe@ucdavis.edu> (supplier of updated rsem package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 27 Aug 2015 13:17:53 -0400 Source: rsem Binary: rsem Architecture: source amd64 Version: 1.2.22+dfsg-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <crusoe@ucdavis.edu> Description: rsem - RNA-Seq by Expectation-Maximization Closes: 778578 Changes: rsem (1.2.22+dfsg-1) unstable; urgency=low . * Initial release (Closes: #778578) Checksums-Sha1: cf4465ffd932acdc4af9afd8adebe557a59bd7b3 1974 rsem_1.2.22+dfsg-1.dsc 9b042597f22ca80c2cd65602ba3e3b187f978653 128327 rsem_1.2.22+dfsg.orig.tar.gz 18ea6b1a85218aab8ad5014c2b90f8fb384e77ba 5728 rsem_1.2.22+dfsg-1.debian.tar.xz aa6bcb9aadd1b6f8ebbb69838027f3653e50e4cc 475010 rsem_1.2.22+dfsg-1_amd64.deb Checksums-Sha256: f2ea8f62bec5be9022420e972af311a90f096dd9e25105b5c6bd0d761e27ff95 1974 rsem_1.2.22+dfsg-1.dsc 72259849fb3303fd9998a9496925a0d4c3cee7b9eb4d2b660d06e9de83ad3651 128327 rsem_1.2.22+dfsg.orig.tar.gz 4feac9bb70392014fc065f251434795a66e10a6ed3f13cbfdacf4be3f5fb560f 5728 rsem_1.2.22+dfsg-1.debian.tar.xz 8a5cae64ce9bef8aa8a02f7b6a84884fb9a46b031c410fa765a9a704b4792f42 475010 rsem_1.2.22+dfsg-1_amd64.deb Files: a232d21f01a1340dc2d92e6a22159280 1974 science optional rsem_1.2.22+dfsg-1.dsc acce30151308dfc3d234a29ead6c3ee1 128327 science optional rsem_1.2.22+dfsg.orig.tar.gz cee89ad822a9501d4cc9d7157d9e5148 5728 science optional rsem_1.2.22+dfsg-1.debian.tar.xz 7b8e85a28b4fedca403a2aac8a7ab369 475010 science optional rsem_1.2.22+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJWJq2AAAoJEFeKBJTRxkbRbpwP/RBvB9H23Nuyoj+U36rlhcsK l7GTpo/ht8l8K2DdZFTa0L+kKGCze8AIYxCo1J74aSAPoZOLG98pu/bIQbopOj2o SvcrRspAz2MqGltuKqv1BIbyRaYtx4magxcJ9ZVB2yFRqBAN0mZRXznbU6VDgau9 SHIMKJ6OyhyPlEvOSUTcOKf0nk5ZPy5urfPJR6cwNRVXRPZM3JlZVbbVjB/yCrSn YOzUXG5ybmQjtaLyaVX30b/E+BZK9XRzfl8RK9K6VtNdUr0ceMVl63AtbDxazsOT FyWV06Cjxzo0TMIwLaNpJag52IPx7bpfDJ5cBXFBBJhk306wqqi5VKnuWgwVPcct 1WSZ9zdxCYQWtLjkBISjVSCbweNmT3xfsmcHjE07tq/iVQ/yqA+8Ax0Zedz716bB 9/LH02ihQ9/Ic6ZnCwV+sPB05P4nvM42U62fQDrLO7pCs2zVVsrqh4jpu/lvw8dZ 8M+q/JuDugGEeNVrf/3AK0C0CbvfxtoJhUHIvuJTmfyTC4m8zQ5KEw70F1+ol/9T snZrPp+A44XykJvfHx5wiJed8U6F7pT9pcsDMwe1ut0ns/c+tP+ZD6AQs8tt9fng A0DBR3KzGqwwfZ61s8Vqnpy2AeFBZzXcNdKZtsRhGqFgJix2t0D/Zz2sQJ672Jb7 Us5tzyUWf+WiBMHTpL/a =Y5hc -----END PGP SIGNATURE-----
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