| 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' |
commit | commitdiff | tree | snapshot |
| 2014-03-21 |
Bo Li | Modified the shebang line for perl scripts |
commit | commitdiff | tree | snapshot |
| 2014-03-21 |
Bo Li | Added support for allele-specific expression estimation |
commit | commitdiff | tree | snapshot |
| 2014-03-09 |
Bo Li | Fixed a typo in rsem-calculate-expression's document... |
commit | commitdiff | tree | snapshot |
| 2014-02-14 |
Bo Li | Added Bowtie 2 support |
commit | commitdiff | tree | snapshot |
| 2014-02-01 |
Bo Li | Fixed a bug which will lead to out-of-memory error... |
commit | commitdiff | tree | snapshot |
| 2014-01-11 |
Bo Li | Removed unnecessary spaces in POD doc of rsem-calculate... |
commit | commitdiff | tree | snapshot |
| 2014-01-09 |
Bo Li | Added update samtools to WHAT_IS_NEW |
commit | commitdiff | tree | snapshot |
| 2014-01-09 |
Bo Li | Modified WHAT_IS_NEW for RSEM v1.2.9 |
commit | commitdiff | tree | snapshot |
| 2014-01-09 |
Bo Li | Fixed a problem that will lead compilation errors for... |
commit | commitdiff | tree | snapshot |
| 2014-01-09 |
Bo Li | README.md is updated |
commit | commitdiff | tree | snapshot |
| 2014-01-09 |
Bo Li | Updated samtools to 0.1.19 |
commit | commitdiff | tree | snapshot |
| 2013-12-02 |
Bo Li | Added a file describing the format of sample_name.stat... |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 2013-09-07 |
Bo Li | Fixed a displaying problem for rsem-run-ebseq's Pod... |
commit | commitdiff | tree | snapshot |
| 2013-09-07 |
Bo Li | Fixed loading library problem for EBSeq/install |
commit | commitdiff | tree | snapshot |
| 2013-09-07 |
Bo Li | Fixed a bug for adding EBSeq's local library path |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 2013-03-22 |
Bo Li | Modified rsem-tbam2gbam so that the original alignment... |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 2013-01-07 |
Bo Li | Modified rsem-find-DE |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 2012-10-18 |
Bo Li | Added --version option for rsem-calculate-expression |
commit | commitdiff | tree | snapshot |
| 2012-10-10 |
Bo Li | use if/elsif to replace switch in rsem-calculate-expression |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 2012-07-23 |
Bo Li | Fixed a bug for calling pthread_join |
commit | commitdiff | tree | snapshot |
| 2012-07-22 |
Bo Li | Fixed a bug in perl scripts for printing error messages |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 2012-04-14 |
Bo Li | Fixed a bug related to intermediate output displaying... |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 2012-03-09 |
Bo Li | Improved warning messages in rsem-gen-transcript-plots |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 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 |
commit | commitdiff | tree | snapshot |
| 2011-12-09 |
Bo Li | convert-sam-for-rsem is updated |
commit | commitdiff | tree | snapshot |
| 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... |
commit | commitdiff | tree | snapshot |
| 2011-11-11 |
Bo Li | some displaying issue in rsem-calculate-expression... |
commit | commitdiff | tree | snapshot |
| 2011-11-11 |
Bo Li | add optional field XS for cufflinks |
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| 2011-11-10 |
Bo Li | rsem v1.1.14, add --sampling-for-bam option, modify... |
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| 2011-11-06 |
Bo Li | rsem v1.1.13, speed up EM by only updating model parame... |
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| 2011-10-19 |
Bo Li | rsem v1.1.12 extract-transcript-to-gene-map-from-trinit... |
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| 2011-10-19 |
Bo Li | rsem v1.1.12, add a script to extract transcript-to... |
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| 2011-08-25 |
Bo Li | rsem v1.1.11, allow spaces appear in field seqname... |
commit | commitdiff | tree | snapshot |
| 2011-08-25 |
Bo Li | rsem v1.1.11 |
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| 2011-08-12 |
Bo Li | fix one bug will lead using not the last theta value... |
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| 2011-08-11 |
Bo Li | rsem v1.2.0 |
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