jonassibbesen/rpvg issues and pull requests

#69 - Gracefully error if --path-info file doesn't exist

Pull Request - State: open - Opened by faithokamoto about 1 month ago

#68 - eeking Guidance on Downstream RNA-Seq Analysis after rpvg expression

Issue - State: open - Opened by CarlosAmadeo7 about 1 month ago

#67 - How to identify variants in haplotypes in rpvg output?

Issue - State: open - Opened by MarzenaMarszalek 2 months ago

#66 - Update libvgio

Pull Request - State: open - Opened by adamnovak 2 months ago

#65 - Error in HaplotypeAbundanceEstimatesWriter

Issue - State: closed - Opened by zhqduan 2 months ago

#64 - Inflate operation failed: invalid distance too far back terminate called after throwing an instance of 'std::runtime_error'

Issue - State: open - Opened by CarlosAmadeo7 4 months ago - 7 comments

#63 - question about fragment size distribiton and error(NestedPathAbundanceEstimator) when using short read illumina RNA seq data.

Issue - State: open - Opened by jjuhyunkim 4 months ago - 3 comments

#62 - Question about usage of rpvg command

Issue - State: open - Opened by CarlosAmadeo7 5 months ago - 11 comments

#61 - rpvg stuck for two days

Issue - State: closed - Opened by Jokendo-collab 9 months ago

#60 - mapping reads to pan-transcriptom too slow

Issue - State: closed - Opened by jkfo002 10 months ago - 2 comments

#59 - HST assignment : rpvg assigned two different homo HST instead of expected heterozygous transcripts.

Issue - State: open - Opened by jjuhyunkim about 1 year ago

#58 - Error : void NestedPathAbundanceEstimator::inferPathSubsetAbundance

Issue - State: closed - Opened by jjuhyunkim about 1 year ago - 2 comments

#57 - Haplotype probability and read count

Issue - State: open - Opened by agolicz over 1 year ago - 2 comments

#56 - Haplotype transcript length inconsistent with GTF

Issue - State: closed - Opened by dongdongdong0203 over 1 year ago - 3 comments

#55 - Meaning of input and output files of pantranscriptome

Issue - State: closed - Opened by dongdongdong0203 over 1 year ago - 5 comments

#54 - Can't run rpvg successfully

Issue - State: closed - Opened by Tonitsk8264 over 1 year ago - 5 comments

#53 - Unable to run rpvg analyses without error

Issue - State: open - Opened by JoshLangman over 1 year ago - 2 comments

#52 - 'std::bad_alloc' error in rpvg

Issue - State: closed - Opened by xuxingyubio over 1 year ago - 3 comments

#51 - Fix infinite loop in fragment length distribution estimation

Pull Request - State: closed - Opened by jeizenga over 1 year ago

#50 - Too much time consumed in quantification

Issue - State: closed - Opened by LiuShang-777 almost 2 years ago - 8 comments

#49 - Problems on pan-transcriptome index

Issue - State: closed - Opened by LiuShang-777 almost 2 years ago - 3 comments

#48 - Failed to read BGZF block data at offset 4088217654 expected 4336 bytes; hread returned 1914

Issue - State: open - Opened by abcyulongwang almost 2 years ago - 3 comments

#47 - Add static build option

Pull Request - State: closed - Opened by jonassibbesen almost 2 years ago

#46 - Unable to obtain GWBT

Issue - State: closed - Opened by ld9866 almost 2 years ago - 13 comments

#45 - How to prepare the gtf?

Issue - State: closed - Opened by ld9866 almost 2 years ago - 7 comments

#44 - Could not install the rpvg in Linux

Issue - State: closed - Opened by ld9866 almost 2 years ago - 2 comments

#43 - Assertion `hasNodeId(node_id)' failed

Issue - State: open - Opened by wtulle almost 2 years ago - 20 comments

#42 - make static version?

Issue - State: open - Opened by LouisPwr about 2 years ago - 2 comments

#41 - Update Catch2 to newer version

Pull Request - State: closed - Opened by jonassibbesen about 2 years ago

#40 - build rpvg failed

Issue - State: closed - Opened by hailingfang about 2 years ago - 1 comment

#39 - Updated dependencies

Pull Request - State: closed - Opened by jonassibbesen about 2 years ago

#38 - Model for rpvg's output

Issue - State: closed - Opened by lsoldini over 2 years ago - 40 comments

#37 - Software for differential expression analysis from rpvg's readcount

Issue - State: closed - Opened by lsoldini over 2 years ago - 4 comments

#36 - Add marginal transcript abundance inference

Pull Request - State: closed - Opened by jonassibbesen over 2 years ago

#35 - gtf error

Issue - State: open - Opened by zxc1359 over 2 years ago - 1 comment

#34 - Crash: Assertion `best_align_score <= optimal_score' failed

Issue - State: closed - Opened by lsoldini over 2 years ago - 4 comments

#33 - Errors while running rpvg

Issue - State: closed - Opened by prenderj almost 3 years ago - 8 comments

#32 - About the compilation and installation of rpvg software

Issue - State: closed - Opened by GeorgeBGM almost 3 years ago - 24 comments

#31 - Update gbwt submodule version

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#30 - Fix parsing of new path info format

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#29 - Added noise to inference and output

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#28 - Fix gam intron parsing issue

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#27 - Added non-quality score and max fragment length options

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#26 - Add joint haplotype-specific expression output

Pull Request - State: closed - Opened by jonassibbesen about 3 years ago

#25 - Optimized the haplotyping step, and added support for allelic mapping qualities and gzipped transcript info files

Pull Request - State: closed - Opened by jonassibbesen over 3 years ago

#24 - Fix numerical issues in skew normal fitting

Pull Request - State: closed - Opened by jeizenga over 3 years ago

#23 - Add skew-normal option for fragment length distribution

Pull Request - State: closed - Opened by jeizenga over 3 years ago

#22 - Added example dataset

Pull Request - State: closed - Opened by jonassibbesen over 3 years ago

#21 - Added maximum score difference threshold to options

Pull Request - State: closed - Opened by jonassibbesen over 3 years ago

#20 - Added haplotyping output to haplotype-transcripts inference mode

Pull Request - State: closed - Opened by jonassibbesen almost 4 years ago

#19 - Improve convergence criteria for lowly expressed transcripts

Pull Request - State: closed - Opened by jonassibbesen almost 4 years ago

#18 - Haplotype probability bug fix and changes to noise usage in expression estimation

Pull Request - State: closed - Opened by jonassibbesen almost 4 years ago

#17 - Added support for r-index, partial matching and improved the noise estimates (first release).

Pull Request - State: closed - Opened by jonassibbesen almost 4 years ago

#16 - Added option to enforce that haplotype estimates are equivalent for transcripts in the same cluster

Pull Request - State: closed - Opened by jonassibbesen about 4 years ago

#15 - Abundance Gibbs sampling bug fix

Pull Request - State: closed - Opened by jonassibbesen about 4 years ago

#14 - Read count bug fix in Gibbs sample output

Pull Request - State: closed - Opened by jonassibbesen about 4 years ago