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2013-03-27	Bo Li	remove .gitignore from the staging area	commit \| commitdiff \| tree
2013-03-22	Bo Li	Added some user-friendly error messages for BamConverter.h	commit \| commitdiff \| tree
2013-03-22	Bo Li	Modified rsem-tbam2gbam so that the original alignment...	commit \| commitdiff \| tree
2013-01-27	Bo Li	Fixed a bug that will lead perl scripts fail to find...	commit \| commitdiff \| tree
2013-01-24	Bo Li	Added user-friendly error messages if users forget...	commit \| commitdiff \| tree
2013-01-08	Bo Li	Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector...	commit \| commitdiff \| tree
2013-01-07	Bo Li	Modified rsem-find-DE	commit \| commitdiff \| tree
2013-01-07	Bo Li	Updated EBSeq to v1.1.5	commit \| commitdiff \| tree
2012-11-30	Bo Li	- Added poly(A) tails to 'reference_name.transcripts...	commit \| commitdiff \| tree
2012-10-21	Bo Li	Updated EBSeq to v1.1.4	commit \| commitdiff \| tree
2012-10-18	Bo Li	Added --version option for rsem-calculate-expression	commit \| commitdiff \| tree
2012-10-10	Bo Li	use if/elsif to replace switch in rsem-calculate-expression	commit \| commitdiff \| tree
2012-09-24	Bo Li	Fixed a bug to make RSEM generated BAM file valid input...	commit \| commitdiff \| tree
2012-09-15	Bo Li	If a gene is not expressed, its length/effective length...	commit \| commitdiff \| tree
2012-09-11	Bo Li	README.md is changed	commit \| commitdiff \| tree
2012-09-11	Bo Li	Added a script, 'rsem-find-DE', to run EBSeq automatically	commit \| commitdiff \| tree
2012-09-10	Bo Li	changed output format to contain FPKM etc. ; fixed...	commit \| commitdiff \| tree
2012-07-27	Bo Li	Added a user-friendly error message for rsem-sam-validator	commit \| commitdiff \| tree
2012-07-23	Bo Li	Fixed a bug for calling pthread_join	commit \| commitdiff \| tree
2012-07-22	Bo Li	Fixed a bug in perl scripts for printing error messages	commit \| commitdiff \| tree
2012-07-15	Bo Li	Fix a bug on convert-sam-for-rsem for the case that...	commit \| commitdiff \| tree
2012-07-02	Bo Li	rsem v1.1.21	commit \| commitdiff \| tree
2012-06-06	Bo Li	Tested the codes	commit \| commitdiff \| tree
2012-06-05	Bo Li	Made the BAM output of RSEM have all information contained...	commit \| commitdiff \| tree
2012-04-26	Bo Li	Included EBSeq for downstream differential expression...	commit \| commitdiff \| tree
2012-04-15	Bo Li	Added some instructions on how to visualize transcript...	commit \| commitdiff \| tree
2012-04-14	Bo Li	Fixed a bug related to intermediate output displaying...	commit \| commitdiff \| tree
2012-04-14	Bo Li	Fixed a bug related to intermediate output displaying...	commit \| commitdiff \| tree
2012-03-21	Bo Li	Allowed > 2^31 hits	commit \| commitdiff \| tree
2012-03-11	Bo Li	Modified makefile to work for gcc version 4.5.3 or...	commit \| commitdiff \| tree
2012-03-11	Bo Li	Modified 'convert-sam-for-rsem' so that this program...	commit \| commitdiff \| tree
2012-03-11	Bo Li	Add a validator for input SAM/BAM file	commit \| commitdiff \| tree
2012-03-09	Bo Li	Improved warning messages in rsem-gen-transcript-plots	commit \| commitdiff \| tree
2012-03-09	Bo Li	Add warning messages for detected invalid alignments	commit \| commitdiff \| tree
2012-02-19	Bo Li	[Change] Do not add --phred33-qual option if --no-qualities...	commit \| commitdiff \| tree
2012-02-09	Bo Li	The order of @SQ tags in SAM/BAM files can be arbitrary now	commit \| commitdiff \| tree
2012-02-08	Bo Li	add --no-bam-output option to not generate output bam...	commit \| commitdiff \| tree
2012-02-08	Bo Li	roll back to original version plus fixed a small bug...	commit \| commitdiff \| tree
2012-02-08	Bo Li	rewrote parallelization of calcCI.cpp	commit \| commitdiff \| tree
2012-01-31	Bo Li	rsem v1.1.16	commit \| commitdiff \| tree
2012-01-26	Bo Li	rsem v1.1.15	commit \| commitdiff \| tree
2012-01-18	Bo Li	rsem v1.1.14	commit \| commitdiff \| tree
2011-12-31	Bo Li	relax the requirement about GTF attribute format	commit \| commitdiff \| tree
2011-12-14	Bo Li	modify one error message and add --bowtie-chunkmbs...	commit \| commitdiff \| tree
2011-12-14	Bo Li	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2011-12-14	Bo Li	another change	commit \| commitdiff \| tree
2011-12-14	bli25wisc	Merge pull request #1 from earonesty/master	commit \| commitdiff \| tree
2011-12-10	Bo Li	updated some description	commit \| commitdiff \| tree
2011-12-10	Bo Li	new update	commit \| commitdiff \| tree
2011-12-09	Bo Li	convert-sam-for-rsem is updated	commit \| commitdiff \| tree
2011-12-09	Bo Li	add a script to convert sam file for non-bowtie aligner	commit \| commitdiff \| tree
2011-12-04	Bo Li	rsem-v1.1.14b3	commit \| commitdiff \| tree
2011-12-02	Bo Li	rsem-1.1.14 with transcript wiggle plot generation	commit \| commitdiff \| tree
2011-12-01	Bo Li	add new files	commit \| commitdiff \| tree
2011-11-28	Bo Li	tested version for tbam2gbam	commit \| commitdiff \| tree
2011-11-11	Bo Li	some displaying issue in rsem-calculate-expression...	commit \| commitdiff \| tree
2011-11-11	Bo Li	add optional field XS for cufflinks	commit \| commitdiff \| tree
2011-11-10	Bo Li	rsem v1.1.14, add --sampling-for-bam option, modify...	commit \| commitdiff \| tree
2011-11-06	Bo Li	rsem v1.1.13, speed up EM by only updating model parameters...	commit \| commitdiff \| tree
2011-10-19	Bo Li	rsem v1.1.12 extract-transcript-to-gene-map-from-trinity...	commit \| commitdiff \| tree
2011-10-19	Bo Li	rsem v1.1.12, add a script to extract transcript-to...	commit \| commitdiff \| tree
2011-08-25	Bo Li	rsem v1.1.11, allow spaces appear in field seqname...	commit \| commitdiff \| tree
2011-08-25	Bo Li	rsem v1.1.11	commit \| commitdiff \| tree
2011-08-12	Bo Li	fix one bug will lead using not the last theta value...	commit \| commitdiff \| tree
2011-08-11	Bo Li	rsem v1.2.0	commit \| commitdiff \| tree
2011-07-26	Bo Li	MAPQ changed	commit \| commitdiff \| tree
2011-05-27	Bo Li	rsem v1.1.9	commit \| commitdiff \| tree
2011-05-24	Bo Li	rsem-plot-model updated	commit \| commitdiff \| tree
2011-04-26	Bo Li	fixed a bug in rsem-plot-model	commit \| commitdiff \| tree
2011-04-25	Bo Li	add feature that jump lines with # in gtf	commit \| commitdiff \| tree
2011-04-25	Bo Li	back to single threaded Gibbs	commit \| commitdiff \| tree
2011-04-25	Bo Li	back to single thread Gibbs	commit \| commitdiff \| tree
2011-04-25	Bo Li	Version with Gibbs parallelized	commit \| commitdiff \| tree
2011-04-21	Bo Li	a bug in simulation.cpp is fixed.	commit \| commitdiff \| tree
2011-04-21	Bo Li	a bug in *?Model.h was fixed.	commit \| commitdiff \| tree
2011-04-19	Bo Li	some changes	commit \| commitdiff \| tree
2011-04-18	Bo Li	RSEM v1.1.8	commit \| commitdiff \| tree
2011-04-18	Bo Li	RSEM v1.1.8	commit \| commitdiff \| tree
2011-04-17	Bo Li	lots of changes	commit \| commitdiff \| tree
2011-04-09	Bo Li	fixed a bug for transcript set as reference	commit \| commitdiff \| tree
2011-04-02	Bo Li	fix a bug in partition reads for parallel	commit \| commitdiff \| tree
2011-03-22	Bo Li	README.md is updated to include C++, Perl and R as...	commit \| commitdiff \| tree
2011-03-18	Bo Li	a bug in rsem-plot-model is fixed	commit \| commitdiff \| tree
2011-03-18	Bo Li	v1.1.5.b	commit \| commitdiff \| tree
2011-03-17	Bo Li	Fixed bugs in the Gibbs sampler. Fixed a bug which...	commit \| commitdiff \| tree
2011-03-15	Bo Li	rsem-plot-model was changed again	commit \| commitdiff \| tree
2011-03-15	Bo Li	rsem-plot-model was modified	commit \| commitdiff \| tree
2011-03-11	Bo Li	rename plotModel.R to rsem-plot-model	commit \| commitdiff \| tree
2011-03-11	Bo Li	README.md changed	commit \| commitdiff \| tree
2011-03-11	Bo Li	Enable RSEM to visualize the model learned from data	commit \| commitdiff \| tree
2011-03-09	Bo Li	Fixed a bug related to output format. Grant read permession...	commit \| commitdiff \| tree
2011-02-21	Bo Li	README.md modified	commit \| commitdiff \| tree
2011-02-21	Bo Li	README.md	commit \| commitdiff \| tree
2011-02-21	Bo Li	README.md modified to display correctly in github	commit \| commitdiff \| tree
2011-02-21	Bo Li	README.md changed	commit \| commitdiff \| tree
2011-02-17	Bo Li	change README.txt to README.md	commit \| commitdiff \| tree
2011-02-17	Bo Li	change README.txt to README.md	commit \| commitdiff \| tree
2011-02-17	Bo Li	v1.1.2	commit \| commitdiff \| tree
2011-02-17	Bo Li	Normalized Read Fraction(nrf) are eliminated from outputs...	commit \| commitdiff \| tree
2011-02-17	Bo Li	Normalized Read Fraction(nrf) are eliminated from outputs...	commit \| commitdiff \| tree
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