Ecosyste.ms: Issues

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GitHub / single-cell-genetics/cellSNP issues and pull requests

#35 - generating VCF for REGION_VCF from RNA-seq data

Issue - State: open - Opened by gebdu over 1 year ago - 1 comment

#23 - Chromosome naming in reference VCF files

Issue - State: closed - Opened by apredeus over 2 years ago - 11 comments

#22 - KeyError: '.' in cellSNP/pileup_utils.py causing failure of temp file merging

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

#21 - add citation

Pull Request - State: closed - Opened by hxj5 about 3 years ago

#20 - Empty AD&DP mtx

Issue - State: closed - Opened by AnjaliC4 over 3 years ago - 23 comments

#19 - AD in cells

Issue - State: open - Opened by penglbio over 3 years ago - 1 comment

#18 - Some SNPs are not in gene

Issue - State: open - Opened by penglbio over 3 years ago - 1 comment

#17 - Does it work for mouse？

Issue - State: closed - Opened by semir2 over 3 years ago - 1 comment

#16 - Wrong number of chromosomes in output file?

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

#15 - Reference Genome

Issue - State: open - Opened by OldManTae almost 4 years ago - 1 comment

#14 - Running cellSNP on transcriptomic BAM from salmon alevin

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

#13 - Change the flag filtering default to include PCR duplicates

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

#12 - Feature count

Pull Request - State: closed - Opened by huangyh09 about 4 years ago

#11 - Fix using qqual and query_alignment_sequence

Pull Request - State: closed - Opened by hxj5 about 4 years ago

#10 - Question about running cellSNP on merged BAM files from multiple samples

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

#9 - Run time estimation

Issue - State: open - Opened by PeteHaitch over 4 years ago - 3 comments

#8 - No SNPs called in more than 1 barcodes

Issue - State: open - Opened by saisomesh2594 over 4 years ago - 3 comments

#7 - output sparse matrix

Issue - State: closed - Opened by bio-la over 4 years ago - 11 comments

#6 - Is it expected to generate a "position x barcode" matrix?

Issue - State: closed - Opened by Griffan almost 5 years ago - 1 comment

#5 - Default nan-handling policy is a memory hog

Issue - State: open - Opened by ivanov-v-v almost 5 years ago - 1 comment

#4 - RuntimeWarning: divide by zero encountered in log

Issue - State: closed - Opened by Griffan about 5 years ago - 9 comments

#3 - Run time estimation

Issue - State: closed - Opened by coh-racng about 5 years ago - 1 comment

#2 - Problem with New Version (0.1.3)

Issue - State: closed - Opened by elderni about 5 years ago - 2 comments

#1 - Optimisation suggestions

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