| 2014-06-05 |
Bo Li | Modified RSEM perl scripts so that RSEM directory will...
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commit | commitdiff | tree |
| 2014-06-05 |
Bo Li | Removed '--no-bowtie' and '--no-ntog' options in 'rsem...
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commit | commitdiff | tree |
| 2014-06-05 |
Bo Li | Generated two index multi-Fasta files instead, one...
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commit | commitdiff | tree |
| 2014-05-27 |
Bo Li | WHAT_IS_NEW is updated
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commit | commitdiff | tree |
| 2014-05-27 |
Bo Li | Changed the behavior of parsing GTF file. Now if a...
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commit | commitdiff | tree |
| 2014-04-03 |
Bo Li | Use PATH env to instead the variable
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commit | commitdiff | tree |
| 2014-03-27 |
Bo Li | Modified the acknowledgement section of README.md
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commit | commitdiff | tree |
| 2014-03-27 |
Bo Li | Modified the transcript extraction behavior of 'rsem...
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commit | commitdiff | tree |
| 2014-03-22 |
Bo Li | Added '--seed' option for 'rsem-simulate-reads'
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commit | commitdiff | tree |
| 2014-03-21 |
Bo Li | Modified the shebang line for perl scripts
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commit | commitdiff | tree |
| 2014-03-21 |
Bo Li | Added support for allele-specific expression estimation
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commit | commitdiff | tree |
| 2014-03-09 |
Bo Li | Fixed a typo in rsem-calculate-expression's document...
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commit | commitdiff | tree |
| 2014-02-14 |
Bo Li | Added Bowtie 2 support
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commit | commitdiff | tree |
| 2014-02-01 |
Bo Li | Fixed a bug which will lead to out-of-memory error...
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commit | commitdiff | tree |
| 2014-01-11 |
Bo Li | Removed unnecessary spaces in POD doc of rsem-calculate...
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commit | commitdiff | tree |
| 2014-01-09 |
Bo Li | Added update samtools to WHAT_IS_NEW
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commit | commitdiff | tree |
| 2014-01-09 |
Bo Li | Modified WHAT_IS_NEW for RSEM v1.2.9
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commit | commitdiff | tree |
| 2014-01-09 |
Bo Li | Fixed a problem that will lead compilation errors for...
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commit | commitdiff | tree |
| 2014-01-09 |
Bo Li | README.md is updated
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commit | commitdiff | tree |
| 2014-01-09 |
Bo Li | Updated samtools to 0.1.19
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commit | commitdiff | tree |
| 2013-12-02 |
Bo Li | Added a file describing the format of sample_name.stat...
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commit | commitdiff | tree |
| 2013-11-22 |
Bo Li | Provided a more detailed description for how to simulate...
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commit | commitdiff | tree |
| 2013-09-25 |
Bo Li | Added a line in WHAT_IS_NEW for renaming of quality...
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commit | commitdiff | tree |
| 2013-09-07 |
Bo Li | Fixed a displaying problem for rsem-run-ebseq's Pod...
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commit | commitdiff | tree |
| 2013-09-07 |
Bo Li | Fixed loading library problem for EBSeq/install
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commit | commitdiff | tree |
| 2013-09-07 |
Bo Li | Fixed a bug for adding EBSeq's local library path
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commit | commitdiff | tree |
| 2013-09-07 |
Bo Li | Changed WHAT_IS_NEW
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commit | commitdiff | tree |
| 2013-09-07 |
Bo Li | 'rsem-run-ebseq': Added 'output_file.condmeans' for...
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commit | commitdiff | tree |
| 2013-09-02 |
Bo Li | Added support for DE analysis on multiple conditions...
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commit | commitdiff | tree |
| 2013-08-28 |
Bo Li | Renamed --phred33-quals, --phred64-quals, and --solexa...
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commit | commitdiff | tree |
| 2013-08-21 |
Bo Li | Fixed a minor bug which only affects paired-end reads...
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commit | commitdiff | tree |
| 2013-07-31 |
Bo Li | Install the latest version of EBSeq from Bioconductor...
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commit | commitdiff | tree |
| 2013-07-04 |
Bo Li | Fixed a bug in rsem-find-DE, which will crash the script...
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commit | commitdiff | tree |
| 2013-06-26 |
Bo Li | Updated EBSeq from v1.1.5 to v1.1.6 and fixed a bug...
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commit | commitdiff | tree |
| 2013-04-15 |
Bo Li | Modifed README.md and WHAT_IS_NEW
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commit | commitdiff | tree |
| 2013-04-15 |
Bo Li | Modified wiggle.cpp & wiggle.h for more accurate floating...
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commit | commitdiff | tree |
| 2013-04-15 |
Bo Li | Modified my_assert.h to postpone error message string...
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commit | commitdiff | tree |
| 2013-04-05 |
Bo Li | Removed a too stringent sanity check in rsem-gen-transcript...
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commit | commitdiff | tree |
| 2013-03-27 |
Bo Li | remove .gitignore from the staging area
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commit | commitdiff | tree |
| 2013-03-22 |
Bo Li | Added some user-friendly error messages for BamConverter.h
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commit | commitdiff | tree |
| 2013-03-22 |
Bo Li | Modified rsem-tbam2gbam so that the original alignment...
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commit | commitdiff | tree |
| 2013-01-27 |
Bo Li | Fixed a bug that will lead perl scripts fail to find...
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commit | commitdiff | tree |
| 2013-01-24 |
Bo Li | Added user-friendly error messages if users forget...
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commit | commitdiff | tree |
| 2013-01-08 |
Bo Li | Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector...
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commit | commitdiff | tree |
| 2013-01-07 |
Bo Li | Modified rsem-find-DE
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commit | commitdiff | tree |
| 2013-01-07 |
Bo Li | Updated EBSeq to v1.1.5
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commit | commitdiff | tree |
| 2012-11-30 |
Bo Li | - Added poly(A) tails to 'reference_name.transcripts...
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commit | commitdiff | tree |
| 2012-10-21 |
Bo Li | Updated EBSeq to v1.1.4
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commit | commitdiff | tree |
| 2012-10-18 |
Bo Li | Added --version option for rsem-calculate-expression
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commit | commitdiff | tree |
| 2012-10-10 |
Bo Li | use if/elsif to replace switch in rsem-calculate-expression
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commit | commitdiff | tree |
| 2012-09-24 |
Bo Li | Fixed a bug to make RSEM generated BAM file valid input...
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commit | commitdiff | tree |
| 2012-09-15 |
Bo Li | If a gene is not expressed, its length/effective length...
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commit | commitdiff | tree |
| 2012-09-11 |
Bo Li | README.md is changed
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commit | commitdiff | tree |
| 2012-09-11 |
Bo Li | Added a script, 'rsem-find-DE', to run EBSeq automatically
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commit | commitdiff | tree |
| 2012-09-10 |
Bo Li | changed output format to contain FPKM etc. ; fixed...
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commit | commitdiff | tree |
| 2012-07-27 |
Bo Li | Added a user-friendly error message for rsem-sam-validator
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commit | commitdiff | tree |
| 2012-07-23 |
Bo Li | Fixed a bug for calling pthread_join
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commit | commitdiff | tree |
| 2012-07-22 |
Bo Li | Fixed a bug in perl scripts for printing error messages
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commit | commitdiff | tree |
| 2012-07-15 |
Bo Li | Fix a bug on convert-sam-for-rsem for the case that...
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commit | commitdiff | tree |
| 2012-07-02 |
Bo Li | rsem v1.1.21
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commit | commitdiff | tree |
| 2012-06-06 |
Bo Li | Tested the codes
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commit | commitdiff | tree |
| 2012-06-05 |
Bo Li | Made the BAM output of RSEM have all information contained...
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commit | commitdiff | tree |
| 2012-04-26 |
Bo Li | Included EBSeq for downstream differential expression...
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commit | commitdiff | tree |
| 2012-04-15 |
Bo Li | Added some instructions on how to visualize transcript...
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commit | commitdiff | tree |
| 2012-04-14 |
Bo Li | Fixed a bug related to intermediate output displaying...
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commit | commitdiff | tree |
| 2012-04-14 |
Bo Li | Fixed a bug related to intermediate output displaying...
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commit | commitdiff | tree |
| 2012-03-21 |
Bo Li | Allowed > 2^31 hits
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commit | commitdiff | tree |
| 2012-03-11 |
Bo Li | Modified makefile to work for gcc version 4.5.3 or...
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commit | commitdiff | tree |
| 2012-03-11 |
Bo Li | Modified 'convert-sam-for-rsem' so that this program...
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commit | commitdiff | tree |
| 2012-03-11 |
Bo Li | Add a validator for input SAM/BAM file
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commit | commitdiff | tree |
| 2012-03-09 |
Bo Li | Improved warning messages in rsem-gen-transcript-plots
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commit | commitdiff | tree |
| 2012-03-09 |
Bo Li | Add warning messages for detected invalid alignments
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commit | commitdiff | tree |
| 2012-02-19 |
Bo Li | [Change] Do not add --phred33-qual option if --no-qualities...
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commit | commitdiff | tree |
| 2012-02-09 |
Bo Li | The order of @SQ tags in SAM/BAM files can be arbitrary now
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commit | commitdiff | tree |
| 2012-02-08 |
Bo Li | add --no-bam-output option to not generate output bam...
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commit | commitdiff | tree |
| 2012-02-08 |
Bo Li | roll back to original version plus fixed a small bug...
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commit | commitdiff | tree |
| 2012-02-08 |
Bo Li | rewrote parallelization of calcCI.cpp
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commit | commitdiff | tree |
| 2012-01-31 |
Bo Li | rsem v1.1.16
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commit | commitdiff | tree |
| 2012-01-26 |
Bo Li | rsem v1.1.15
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commit | commitdiff | tree |
| 2012-01-18 |
Bo Li | rsem v1.1.14
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commit | commitdiff | tree |
| 2011-12-31 |
Bo Li | relax the requirement about GTF attribute format
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commit | commitdiff | tree |
| 2011-12-14 |
Bo Li | modify one error message and add --bowtie-chunkmbs...
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commit | commitdiff | tree |
| 2011-12-14 |
Bo Li | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2011-12-14 |
Bo Li | another change
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commit | commitdiff | tree |
| 2011-12-10 |
Bo Li | updated some description
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commit | commitdiff | tree |
| 2011-12-10 |
Bo Li | new update
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commit | commitdiff | tree |
| 2011-12-09 |
Bo Li | convert-sam-for-rsem is updated
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commit | commitdiff | tree |
| 2011-12-09 |
Bo Li | add a script to convert sam file for non-bowtie aligner
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commit | commitdiff | tree |
| 2011-12-04 |
Bo Li | rsem-v1.1.14b3
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commit | commitdiff | tree |
| 2011-12-02 |
Bo Li | rsem-1.1.14 with transcript wiggle plot generation
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commit | commitdiff | tree |
| 2011-12-01 |
Bo Li | add new files
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commit | commitdiff | tree |
| 2011-11-28 |
Bo Li | tested version for tbam2gbam
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commit | commitdiff | tree |
| 2011-11-11 |
Bo Li | some displaying issue in rsem-calculate-expression...
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commit | commitdiff | tree |
| 2011-11-11 |
Bo Li | add optional field XS for cufflinks
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commit | commitdiff | tree |
| 2011-11-10 |
Bo Li | rsem v1.1.14, add --sampling-for-bam option, modify...
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commit | commitdiff | tree |
| 2011-11-06 |
Bo Li | rsem v1.1.13, speed up EM by only updating model parameters...
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commit | commitdiff | tree |
| 2011-10-19 |
Bo Li | rsem v1.1.12 extract-transcript-to-gene-map-from-trinity...
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commit | commitdiff | tree |
| 2011-10-19 |
Bo Li | rsem v1.1.12, add a script to extract transcript-to...
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commit | commitdiff | tree |
| 2011-08-25 |
Bo Li | rsem v1.1.11, allow spaces appear in field seqname...
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commit | commitdiff | tree |
| 2011-08-25 |
Bo Li | rsem v1.1.11
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commit | commitdiff | tree |
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