velocyto-team/velocyto.py issues and pull requests

#266 - Is there filter cell in the count process?

Issue - State: open - Opened by hahia about 4 years ago - 1 comment

#264 - Failed to install velocyto.py

Issue - State: open - Opened by Sa753 over 4 years ago - 13 comments

#261 - velocyto run bam file error

Issue - State: closed - Opened by rsggsr over 4 years ago - 5 comments

#259 - Some problem about Dropseq data

Issue - State: open - Opened by hahia over 4 years ago - 1 comment

#252 - ModuleNotFoundError: No module named 'velocyto.speedboosted'

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

#250 - OSError: no BGZF EOF marker; file may be truncated

Issue - State: closed - Opened by grimwoo over 4 years ago - 6 comments

#248 - Pre_filtering of 10X RNAseq loom data from velocyto.py

Issue - State: open - Opened by SiyiWanggou over 4 years ago - 1 comment

#246 - Can not locate the barcodes.tsv file

Issue - State: closed - Opened by grimwoo over 4 years ago - 8 comments

#243 - zero unspliced mRNA

Issue - State: open - Opened by justin-malin over 4 years ago - 1 comment

#241 - CellID in ca does not match the imported TSNE and cluster from cellranger files

Issue - State: open - Opened by therealgenna over 4 years ago - 1 comment

#233 - Artificial gene detection problem

Issue - State: open - Opened by valnymartin almost 5 years ago - 8 comments

#229 - How to reach the genes that are filtered because they are not shared in spliced-unspliced data

Issue - State: open - Opened by selifeski almost 5 years ago - 3 comments

#225 - Problem with the exon number feature on gtf file

Issue - State: closed - Opened by SamueleSoraggi almost 5 years ago - 2 comments

#224 - Error with dropEst->velocyto workflow

Issue - State: open - Opened by jeremymsimon almost 5 years ago - 6 comments

#217 - calculating convolved matrices ... Error in intI(i, n = d[1], dn[[1]], give.dn = FALSE)

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

#215 - Running velocyto on local Mac with 16 gb ram

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

#213 - Velocyto python analysis tutorial error

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

#209 - FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future

Issue - State: open - Opened by zonglunli7515 about 5 years ago - 5 comments

#208 - Memory Error

Issue - State: closed - Opened by annajbott about 5 years ago - 4 comments

#196 - Mismatch between cells in column_attributes and count matrix

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

#194 - 'VelocytoLoom' object has no attribute 'colorandum'

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

#192 - Issues running velocyto

Issue - State: open - Opened by roofya over 5 years ago - 9 comments

#185 - The bam file does not contain cell and umi barcodes appropriately formatted.(use SRP129388 human week 10 fetal forebrain dataset in your paper )

Issue - State: open - Opened by songxiaoning over 5 years ago - 12 comments

#184 - merge two loom file into one loom

Issue - State: closed - Opened by wupeng2 over 5 years ago - 2 comments

#183 - index error list out of range

Issue - State: open - Opened by rekham1077 over 5 years ago - 7 comments

#181 - AttributeError: 'NoneType' object has no attribute 'group', (gif file about Macaca)

Issue - State: open - Opened by ogujessica over 5 years ago - 1 comment

#178 - ValueError: Main matrix cannot be empty

Issue - State: open - Opened by lelesama over 5 years ago - 10 comments

#173 - Issue with group_constraint option in knn_imputation

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

#169 - 'show.velocity.on.embedding.cor' error

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

#165 - Memory requirements for 35000 cells (or more) and how to reduce them

Issue - State: closed - Opened by Clara22 almost 6 years ago - 11 comments

#164 - Empty .loom file?

Issue - State: open - Opened by idalarsson almost 6 years ago - 1 comment

#163 - Issues running velocyto

Issue - State: open - Opened by shabs24 almost 6 years ago - 12 comments

#159 - Execution time for 10X samples

Issue - State: closed - Opened by idalarsson almost 6 years ago - 6 comments

#151 - CellID does not match between scanpy and velocyto

Issue - State: open - Opened by VickyDB almost 6 years ago - 4 comments

#145 - YFP reporter lacking exon_number

Issue - State: closed - Opened by jayypaul almost 6 years ago - 7 comments

#144 - run command fails due to write permissions

Issue - State: open - Opened by gabprg almost 6 years ago - 4 comments

#142 - No unspliced mRNA

Issue - State: closed - Opened by KatjaRM almost 6 years ago - 4 comments

#135 - run10x multiple sample

Issue - State: open - Opened by galib36 almost 6 years ago - 11 comments

#119 - Sample Bam File

Issue - State: open - Opened by shaaaarpy about 6 years ago - 3 comments

#117 - GTF error with no reasons ! IndexError: list index out of range

Issue - State: closed - Opened by Suger0917 about 6 years ago - 7 comments

#115 - MemoryError when generating data table

Issue - State: closed - Opened by tpentim about 6 years ago - 7 comments

#111 - samtools dependency

Issue - State: open - Opened by igordot about 6 years ago - 14 comments

#110 - TypeError: create() got an unexpected keyword argument 'matrix'

Issue - State: open - Opened by snower2010 about 6 years ago - 26 comments

#108 - Installation problem

Issue - State: open - Opened by kiter2520 about 6 years ago - 6 comments

#107 - Bam file does not contain cell and umi barcodes appropriatelly formatted (Run on modified Smart-seq2 protocol)

Issue - State: open - Opened by Suger0917 about 6 years ago - 9 comments

#106 - no BGZF EOF marker; file may be truncated

Issue - State: open - Opened by Linda-Lan about 6 years ago - 7 comments

#86 - Directory "cell" does not exist; Invalid value for "bamfile": Path "cell" does not exist.

Issue - State: closed - Opened by wen-zhou-caltech over 6 years ago - 20 comments

GitHub / velocyto-team/velocyto.py issues and pull requests