Ecosyste.ms: Issues

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GitHub / pachterlab/kallistobustools issues and pull requests

#62 - Error while quantifying with multi-mapping (-mm) option

Issue - State: closed - Opened by jaiganeshjg 6 months ago - 1 comment

#62 - Error while quantifying with multi-mapping (-mm) option

Issue - State: closed - Opened by jaiganeshjg 6 months ago - 1 comment

#61 - .h5ad file does not contain layers spliced and unspliced

Issue - State: open - Opened by mdu4003 7 months ago - 2 comments

#58 - kb count error with CSP reads

Issue - State: closed - Opened by kaijli 9 months ago

#58 - kb count error with CSP reads

Issue - State: closed - Opened by kaijli 9 months ago

#57 - Issue with kb count

Issue - State: open - Opened by lucasinchausti 11 months ago - 3 comments

#57 - Issue with kb count

Issue - State: open - Opened by lucasinchausti 11 months ago - 3 comments

#55 - Improving speed when running `kb count`

Issue - State: open - Opened by reetm09 about 1 year ago - 3 comments

#55 - Improving speed when running `kb count`

Issue - State: open - Opened by reetm09 about 1 year ago - 3 comments

#53 - Running time

Issue - State: open - Opened by BenjaminDEMAILLE over 1 year ago

#53 - Running time

Issue - State: open - Opened by BenjaminDEMAILLE over 1 year ago

#52 - issue with pip install kb-python

Issue - State: open - Opened by dsmolina over 1 year ago

#51 - how to implement EM using kb?

Issue - State: open - Opened by jc271828 over 1 year ago - 2 comments

#51 - how to implement EM using kb?

Issue - State: open - Opened by jc271828 over 1 year ago - 2 comments

#50 - Why is there a big difference between kallisto and cellranger count result？

Issue - State: open - Opened by aizhimin almost 2 years ago - 6 comments

#50 - Why is there a big difference between kallisto and cellranger count result？

Issue - State: open - Opened by aizhimin almost 2 years ago - 6 comments

#49 - kb count subprocess.CalledProcessError:

Issue - State: closed - Opened by victorcat4 almost 2 years ago - 2 comments

#49 - kb count subprocess.CalledProcessError:

Issue - State: closed - Opened by victorcat4 almost 2 years ago - 2 comments

#48 - How to get isoform counts for single cell RNA-seq data?

Issue - State: open - Opened by biopzhang about 2 years ago - 3 comments

#48 - How to get isoform counts for single cell RNA-seq data?

Issue - State: open - Opened by biopzhang about 2 years ago - 3 comments

#47 - Recommendation for alignment visualization

Issue - State: open - Opened by jkniehaus about 2 years ago - 1 comment

#47 - Recommendation for alignment visualization

Issue - State: open - Opened by jkniehaus about 2 years ago - 1 comment

#45 - kallisto bustools with reference transcriptome

Issue - State: open - Opened by MartaBenegas about 2 years ago - 5 comments

#45 - kallisto bustools with reference transcriptome

Issue - State: open - Opened by MartaBenegas about 2 years ago - 5 comments

#44 - kb ref returns empty 'to be generated' files

Issue - State: closed - Opened by liliay about 2 years ago - 9 comments

#44 - kb ref returns empty 'to be generated' files

Issue - State: closed - Opened by liliay about 2 years ago - 9 comments

#41 - update deprecated --lamanno option with the --workflow lamanno option

Pull Request - State: open - Opened by erguntiryaki over 2 years ago - 1 comment

#41 - update deprecated --lamanno option with the --workflow lamanno option

Pull Request - State: open - Opened by erguntiryaki over 2 years ago - 1 comment

#40 - Mito genes not having '-' in the t2g.txt

Issue - State: closed - Opened by GabyBG over 2 years ago - 5 comments

#40 - Mito genes not having '-' in the t2g.txt

Issue - State: closed - Opened by GabyBG over 2 years ago - 5 comments

#39 - RNA Velocity

Issue - State: open - Opened by FionaMoon over 2 years ago

#39 - RNA Velocity

Issue - State: open - Opened by FionaMoon over 2 years ago

#38 - Required files for technology = smartseq2

Issue - State: open - Opened by ostkampp over 2 years ago - 3 comments

#38 - Required files for technology = smartseq2

Issue - State: open - Opened by ostkampp over 2 years ago - 3 comments

#37 - How to provide read1 and read2 fastq files from two lanes to `kb count`?

Issue - State: closed - Opened by naity2 over 2 years ago - 2 comments

#37 - How to provide read1 and read2 fastq files from two lanes to `kb count`?

Issue - State: closed - Opened by naity2 over 2 years ago - 2 comments

#36 - Rhapsody addition?

Issue - State: open - Opened by theheking over 2 years ago - 3 comments

#36 - Rhapsody addition?

Issue - State: open - Opened by theheking over 2 years ago - 3 comments

#35 - Quantify ARC-v1 data

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

#35 - Quantify ARC-v1 data

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

#34 - Hardcoded whitelists

Issue - State: closed - Opened by apredeus almost 3 years ago - 5 comments

#34 - Hardcoded whitelists

Issue - State: closed - Opened by apredeus almost 3 years ago - 5 comments

#32 - How to filter/subset cells for RNA Velocity from kb?

Issue - State: closed - Opened by SimoniMD almost 3 years ago - 1 comment

#32 - How to filter/subset cells for RNA Velocity from kb?

Issue - State: closed - Opened by SimoniMD almost 3 years ago - 1 comment

#30 - Cannot install kb using pip

Issue - State: closed - Opened by ekernf01 almost 3 years ago - 2 comments

#30 - Cannot install kb using pip

Issue - State: closed - Opened by ekernf01 almost 3 years ago - 2 comments

#29 - Problem running kb count w/ multiple intron files

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

#28 - Splitting multimapping read with EM algorithm

Issue - State: closed - Opened by joycekang over 3 years ago - 2 comments

#28 - Splitting multimapping read with EM algorithm

Issue - State: closed - Opened by joycekang over 3 years ago - 2 comments

#27 - Visium tutorial

Pull Request - State: open - Opened by lambdamoses over 3 years ago - 1 comment

#27 - Visium tutorial

Pull Request - State: open - Opened by lambdamoses over 3 years ago - 1 comment

#25 - Different splice abundances than kb tutorial

Issue - State: open - Opened by carbycrab over 3 years ago

#25 - Different splice abundances than kb tutorial

Issue - State: open - Opened by carbycrab over 3 years ago

#24 - error message tracing back to get_kallisto_version

Issue - State: closed - Opened by sanjayrsrivatsan over 3 years ago - 1 comment

#21 - mitochondrial gene filtering

Issue - State: open - Opened by AuroreCapillon over 3 years ago

#20 - Keyboard interrupt error

Issue - State: closed - Opened by kdhkiani almost 4 years ago

#20 - Keyboard interrupt error

Issue - State: closed - Opened by kdhkiani almost 4 years ago

#19 - 0 reads pseudoaligned[~warn] no reads pseudoaligned

Issue - State: closed - Opened by kaizen89 almost 4 years ago - 2 comments

#19 - 0 reads pseudoaligned[~warn] no reads pseudoaligned

Issue - State: closed - Opened by kaizen89 almost 4 years ago - 2 comments

#15 - How does Kallisto bus tools handle multi-mapping reads?

Issue - State: closed - Opened by kikegoni about 4 years ago - 6 comments

#15 - How does Kallisto bus tools handle multi-mapping reads?

Issue - State: closed - Opened by kikegoni about 4 years ago - 6 comments

#14 - How to specify -x with a new technology

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

#13 - kallistobus for MARSseq data

Issue - State: closed - Opened by ogandril over 4 years ago - 3 comments

#12 - Multiple sequensing runs

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

#12 - Multiple sequensing runs

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

#11 - kallisto bus is not avaialble

Issue - State: closed - Opened by liu-xingliang over 4 years ago - 1 comment

#11 - kallisto bus is not avaialble

Issue - State: closed - Opened by liu-xingliang over 4 years ago - 1 comment

#10 - URL Down

Issue - State: closed - Opened by YogiOnBioinformatics over 4 years ago - 3 comments

#10 - URL Down

Issue - State: closed - Opened by YogiOnBioinformatics over 4 years ago - 3 comments

#8 - RNA isoform/alternative splicing analysis

Issue - State: open - Opened by grimwoo over 4 years ago - 5 comments

#7 - kallisto rna velocity RCPP issue

Issue - State: closed - Opened by yaolutian almost 5 years ago - 3 comments

#6 - Create LICENSE

Pull Request - State: closed - Opened by lakigigar almost 5 years ago

#5 - Merge when kb is bumped to 0.24.5

Pull Request - State: closed - Opened by Lioscro about 5 years ago

#4 - Update link to bioRxiv to current version

Pull Request - State: closed - Opened by agdenadel about 5 years ago

#3 - Fix link to velocity index tutorial

Pull Request - State: closed - Opened by zouter over 5 years ago

#2 - https://kallistobus.tools/ down?

Issue - State: closed - Opened by PeteHaitch over 5 years ago - 2 comments

#1 - Whitelist link broken

Issue - State: closed - Opened by Gibbsdavidl over 5 years ago - 1 comment