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rsem.git
2014-06-06
Bo Li
Added posterior standard deviation of counts as output...
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2014-06-06
Bo Li
Added --seed option to set random number generator...
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2014-06-05
Bo Li
Modified RSEM perl scripts so that RSEM directory will...
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2014-06-05
Bo Li
Removed '--no-bowtie' and '--no-ntog' options in 'rsem...
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2014-06-05
Bo Li
Generated two index multi-Fasta files instead, one...
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2014-05-27
Bo Li
WHAT_IS_NEW is updated
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2014-05-27
Bo Li
Changed the behavior of parsing GTF file. Now if a...
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2014-04-03
Bo Li
Use PATH env to instead the variable
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2014-03-27
Bo Li
Modified the acknowledgement section of README.md
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2014-03-27
Bo Li
Modified the transcript extraction behavior of 'rsem...
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2014-03-22
Bo Li
Added '--seed' option for 'rsem-simulate-reads'
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2014-03-21
Bo Li
Modified the shebang line for perl scripts
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2014-03-21
Bo Li
Added support for allele-specific expression estimation
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2014-03-09
Bo Li
Fixed a typo in rsem-calculate-expression's document...
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2014-02-14
Bo Li
Added Bowtie 2 support
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2014-02-01
Bo Li
Fixed a bug which will lead to out-of-memory error...
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2014-01-11
Bo Li
Removed unnecessary spaces in POD doc of rsem-calculate...
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2014-01-09
Bo Li
Added update samtools to WHAT_IS_NEW
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2014-01-09
Bo Li
Modified WHAT_IS_NEW for RSEM v1.2.9
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2014-01-09
Bo Li
Fixed a problem that will lead compilation errors for...
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2014-01-09
Bo Li
README.md is updated
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2014-01-09
Bo Li
Updated samtools to 0.1.19
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2013-12-02
Bo Li
Added a file describing the format of sample_name.stat...
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2013-11-22
Bo Li
Provided a more detailed description for how to simulat...
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2013-09-25
Bo Li
Added a line in WHAT_IS_NEW for renaming of quality...
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2013-09-07
Bo Li
Fixed a displaying problem for rsem-run-ebseq's Pod...
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2013-09-07
Bo Li
Fixed loading library problem for EBSeq/install
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2013-09-07
Bo Li
Fixed a bug for adding EBSeq's local library path
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2013-09-07
Bo Li
Changed WHAT_IS_NEW
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2013-09-07
Bo Li
'rsem-run-ebseq': Added 'output_file.condmeans' for...
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2013-09-02
Bo Li
Added support for DE analysis on multiple conditions...
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2013-08-28
Bo Li
Renamed --phred33-quals, --phred64-quals, and --solexa...
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2013-08-21
Bo Li
Fixed a minor bug which only affects paired-end reads...
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2013-07-31
Bo Li
Install the latest version of EBSeq from Bioconductor...
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2013-07-04
Bo Li
Fixed a bug in rsem-find-DE, which will crash the scrip...
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2013-06-26
Bo Li
Updated EBSeq from v1.1.5 to v1.1.6 and fixed a bug...
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2013-04-15
Bo Li
Modifed README.md and WHAT_IS_NEW
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2013-04-15
Bo Li
Modified wiggle.cpp & wiggle.h for more accurate floati...
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2013-04-15
Bo Li
Modified my_assert.h to postpone error message string...
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2013-04-05
Bo Li
Removed a too stringent sanity check in rsem-gen-transc...
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2013-03-27
Bo Li
remove .gitignore from the staging area
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2013-03-22
Bo Li
Added some user-friendly error messages for BamConverter.h
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2013-03-22
Bo Li
Modified rsem-tbam2gbam so that the original alignment...
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2013-01-27
Bo Li
Fixed a bug that will lead perl scripts fail to find...
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2013-01-24
Bo Li
Added user-friendly error messages if users forget...
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2013-01-08
Bo Li
Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector...
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2013-01-07
Bo Li
Modified rsem-find-DE
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2013-01-07
Bo Li
Updated EBSeq to v1.1.5
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2012-11-30
Bo Li
- Added poly(A) tails to 'reference_name.transcripts...
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2012-10-21
Bo Li
Updated EBSeq to v1.1.4
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2012-10-18
Bo Li
Added --version option for rsem-calculate-expression
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2012-10-10
Bo Li
use if/elsif to replace switch in rsem-calculate-expression
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2012-09-24
Bo Li
Fixed a bug to make RSEM generated BAM file valid input...
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2012-09-15
Bo Li
If a gene is not expressed, its length/effective length...
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2012-09-11
Bo Li
README.md is changed
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2012-09-11
Bo Li
Added a script, 'rsem-find-DE', to run EBSeq automatically
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2012-09-10
Bo Li
changed output format to contain FPKM etc. ; fixed...
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2012-07-27
Bo Li
Added a user-friendly error message for rsem-sam-validator
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2012-07-23
Bo Li
Fixed a bug for calling pthread_join
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2012-07-22
Bo Li
Fixed a bug in perl scripts for printing error messages
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2012-07-15
Bo Li
Fix a bug on convert-sam-for-rsem for the case that...
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2012-07-02
Bo Li
rsem v1.1.21
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2012-06-06
Bo Li
Tested the codes
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2012-06-05
Bo Li
Made the BAM output of RSEM have all information contai...
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2012-04-26
Bo Li
Included EBSeq for downstream differential expression...
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2012-04-15
Bo Li
Added some instructions on how to visualize transcript...
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2012-04-14
Bo Li
Fixed a bug related to intermediate output displaying...
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2012-04-14
Bo Li
Fixed a bug related to intermediate output displaying...
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2012-03-21
Bo Li
Allowed > 2^31 hits
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2012-03-11
Bo Li
Modified makefile to work for gcc version 4.5.3 or...
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2012-03-11
Bo Li
Modified 'convert-sam-for-rsem' so that this program...
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2012-03-11
Bo Li
Add a validator for input SAM/BAM file
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2012-03-09
Bo Li
Improved warning messages in rsem-gen-transcript-plots
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2012-03-09
Bo Li
Add warning messages for detected invalid alignments
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2012-02-27
Colin Dewey
Added .gitignore to ignore build products
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2012-02-27
Colin Dewey
Modified build rules for sam/libbam.a to enable paralle...
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2012-02-19
Bo Li
[Change] Do not add --phred33-qual option if --no-quali...
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2012-02-09
Bo Li
The order of @SQ tags in SAM/BAM files can be arbitrary now
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2012-02-08
Bo Li
add --no-bam-output option to not generate output bam...
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2012-02-08
Bo Li
roll back to original version plus fixed a small bug...
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2012-02-08
Bo Li
rewrote parallelization of calcCI.cpp
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2012-01-31
Bo Li
rsem v1.1.16
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2012-01-26
Bo Li
rsem v1.1.15
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2012-01-18
Bo Li
rsem v1.1.14
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2011-12-31
Bo Li
relax the requirement about GTF attribute format
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2011-12-14
Bo Li
modify one error message and add --bowtie-chunkmbs...
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2011-12-14
Bo Li
Merge remote-tracking branch 'origin/master'
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2011-12-14
Bo Li
another change
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2011-12-14
bli25wisc
Merge pull request #1 from earonesty/master
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2011-12-14
Erik Aronesty
--bowtie-chunkmbs
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2011-12-10
Bo Li
updated some description
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2011-12-10
Bo Li
new update
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2011-12-09
Bo Li
convert-sam-for-rsem is updated
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2011-12-09
Bo Li
add a script to convert sam file for non-bowtie aligner
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2011-12-04
Bo Li
rsem-v1.1.14b3
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2011-12-02
Bo Li
rsem-1.1.14 with transcript wiggle plot generation
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2011-12-01
Bo Li
add new files
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2011-11-28
Bo Li
tested version for tbam2gbam
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2011-11-16
Colin Dewey
Refactored wiggle code and added rsem-bam2readdepth...
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2011-11-11
Bo Li
some displaying issue in rsem-calculate-expression...
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