cortes-ciriano-lab SComatic issues

cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data

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Plotting 96 trinucleotide mutation count

#67 hl-xue opened 2 weeks ago
0
Step4.2 fails to output any variants from scATACseq data

#66 archieandrews10 opened 2 weeks ago
5
How to estimate single-cell mutational burdens

#65 xyzheng123 opened 1 month ago
3
Add max_depth option for pysam.pileup in BaseCellCounter.py and SingleCellGenotype.py

#64 ArthurDondi closed 1 month ago
0
pysam.pileup low max depth leads to FP

#63 ArthurDondi closed 1 month ago
5
Using chromosome reference in Scomatic

#62 Arsamat closed 2 months ago
1
output of SingleCellGenotype is empty!

#61 dipingxian431 closed 1 month ago
6
start > stop

#60 xuxif closed 1 month ago
1
Issue with betabinomial estimation?

#59 danieljrichard opened 3 months ago
1
The problem of analysing single-cell data from multiple tissues of the same individual

#58 zhoudreames opened 5 months ago
1
Matching SNP to cell barcode

#57 malonzm1 closed 1 month ago
1
If the Scomatic could provide the variant allele frequency of unique cell

#56 luhuan93 opened 5 months ago
0
how does input the tsv file to MutationalPatterns

#55 dipingxian431 opened 6 months ago
0
How to remove the influence of different cell numbers

#54 xinghua1001 opened 7 months ago
0
Understanding step 4.2 variant filters

#53 bkinnersley opened 7 months ago
1
How does SingleCellGenotype.py work and what does it mean if substantial number of cell have different expected and observed cell types?

#52 prakashraaz opened 7 months ago
0
Mutational Burden Calculation

#51 JakeJackson22 opened 7 months ago
0
minimal number of cells required for each cell type

#50 rosaranli opened 8 months ago
0
run SComatic with not FACS-sorted data

#49 giorgiagandolfi opened 8 months ago
0
Issue while generating a custom PoN file

#48 Swap90 opened 8 months ago
2
Concurrent running of cells for step 2.

#47 JakeJackson22 closed 8 months ago
2
Does SComatic identify frameshift mutations?

#46 FranSoriano closed 9 months ago
2
Very low number of matched variants when comparing known SNVs from several studies with the results obtained by SComatic when applied to the same data

#45 FranSoriano opened 9 months ago
4
How to separate normal and cancer cells from the same cell type?

#44 cv55 opened 10 months ago
0
Problem installing SComatic

#43 malonzm1 closed 8 months ago
2
hg38 fa recommendation

#42 malonzm1 closed 9 months ago
1
Two questions; about 'Cell_type_noise' filter and MT mutation calling

#41 leehs96 opened 10 months ago
1
SComatic with a single cell type but with germline reference

#40 northerngasc opened 11 months ago
0
Why is the default value of the parameter "min_mq" 255

#39 Topigs closed 9 months ago
1
Challenges with adapting for long read data?

#38 tsa4002 closed 9 months ago
2
A question about the script "BaseCellCalling.step1.py"

#37 sdzxzh closed 11 months ago
0
Do I need estimate new Beta binomial parameters for each sample? Another: according to somatic mutation in epi cells select cancer cell

#36 gloriafight opened 11 months ago
0
Split Bam Error 2

#35 sph17 closed 12 months ago
2
How to run the tool on multiple samples from the same patient

#34 MigleMi opened 12 months ago
0
TrinucleotideContextBackground.py - No such file or directory!

#33 lipikakalson closed 1 year ago
16
How to convert to standard vcf format to be used for downstream analyses?

#32 lipikakalson closed 1 year ago
1
No base count matrix(.tsv) files in Step 2 output but bam files of those cell types are there in Step1 Output.

#31 lipikakalson closed 1 year ago
16
Code for columns of the single cell level genotype result

#30 lijiang825 closed 12 months ago
5
When running scATAC data, No temporary files found in BaseCellCounter.py

#29 nieyage closed 1 year ago
1
ValueError: invalid coordinates: start > stop

#28 amdqiao1 closed 1 year ago
6
chromosome name difference, e.g., chr1 vs 1

#27 robinycfang closed 11 months ago
2
Can you run SComatic on bulk RNA seq?

#26 sph17 closed 1 year ago
1
package ‘VGAM’ is not available (for R version 3.6.1)

#25 FionaMoon closed 1 year ago
1
How SComatic distinguishes between somatic and germline variants?

#24 vladimirkovacevic closed 1 year ago
3
Output of GetAllCallableSites.py for mutational burdens

#23 YiqunCao closed 1 year ago
4
Run SComatic with a matched normal single-cell RNA-seq data

#22 gongyuTang123 closed 1 year ago
1
SComatic on Stereo-seq data

#21 vladimirkovacevic closed 1 year ago
2
invalid contig `1`

#20 ramashka328 closed 1 year ago
4
How to use on data with single cell type

#19 cutleraging closed 1 year ago
3
AttributeError: 'pysam.calignedsegment.PileupColumn' object has no attribute 'get_num_aligned' is occurred in step2

#18 yasuhikohaga closed 1 year ago
8