cortes-ciriano-lab SComatic issues

cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data

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Issue with betabinomial estimation?

#59 danieljrichard opened 1 day ago
0
The problem of analysing single-cell data from multiple tissues of the same individual

#58 zhoudreames opened 1 month ago
1
Matching SNP to cell barcode

#57 malonzm1 opened 2 months ago
0
If the Scomatic could provide the variant allele frequency of unique cell

#56 luhuan93 opened 2 months ago
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how does input the tsv file to MutationalPatterns

#55 dipingxian431 opened 2 months ago
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How to remove the influence of different cell numbers

#54 xinghua1001 opened 3 months ago
0
Understanding step 4.2 variant filters

#53 bkinnersley opened 4 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 4 months ago
0
Mutational Burden Calculation

#51 JakeJackson22 opened 4 months ago
0
minimal number of cells required for each cell type

#50 rosaranli opened 4 months ago
0
run SComatic with not FACS-sorted data

#49 giorgiagandolfi opened 4 months ago
0
Issue while generating a custom PoN file

#48 Swap90 opened 5 months ago
1
Concurrent running of cells for step 2.

#47 JakeJackson22 closed 5 months ago
2
Does SComatic identify frameshift mutations?

#46 FranSoriano closed 6 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 6 months ago
4
How to separate normal and cancer cells from the same cell type?

#44 cv55 opened 7 months ago
0
Problem installing SComatic

#43 malonzm1 closed 5 months ago
1
hg38 fa recommendation

#42 malonzm1 closed 6 months ago
1
Two questions; about 'Cell_type_noise' filter and MT mutation calling

#41 leehs96 opened 7 months ago
1
SComatic with a single cell type but with germline reference

#40 northerngasc opened 7 months ago
0
Why is the default value of the parameter "min_mq" 255

#39 Topigs closed 6 months ago
1
Challenges with adapting for long read data?

#38 tsa4002 closed 6 months ago
2
A question about the script "BaseCellCalling.step1.py"

#37 sdzxzh closed 8 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 8 months ago
0
Split Bam Error 2

#35 sph17 closed 8 months ago
2
How to run the tool on multiple samples from the same patient

#34 MigleMi opened 8 months ago
0
TrinucleotideContextBackground.py - No such file or directory!

#33 lipikakalson closed 8 months ago
16
How to convert to standard vcf format to be used for downstream analyses?

#32 lipikakalson closed 8 months 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 8 months ago
16
Code for columns of the single cell level genotype result

#30 lijiang825 closed 8 months ago
5
When running scATAC data, No temporary files found in BaseCellCounter.py

#29 nieyage closed 9 months ago
1
ValueError: invalid coordinates: start > stop

#28 amdqiao1 closed 8 months ago
6
chromosome name difference, e.g., chr1 vs 1

#27 robinycfang closed 8 months ago
2
Can you run SComatic on bulk RNA seq?

#26 sph17 closed 10 months ago
1
package ‘VGAM’ is not available (for R version 3.6.1)

#25 FionaMoon closed 10 months ago
1
How SComatic distinguishes between somatic and germline variants?

#24 vladimirkovacevic closed 10 months ago
3
Output of GetAllCallableSites.py for mutational burdens

#23 YiqunCao closed 10 months ago
4
Run SComatic with a matched normal single-cell RNA-seq data

#22 gongyuTang123 closed 9 months ago
1
SComatic on Stereo-seq data

#21 vladimirkovacevic closed 11 months ago
2
invalid contig `1`

#20 ramashka328 closed 10 months ago
4
How to use on data with single cell type

#19 cutleraging closed 10 months ago
3
AttributeError: 'pysam.calignedsegment.PileupColumn' object has no attribute 'get_num_aligned' is occurred in step2

#18 yasuhikohaga closed 10 months ago
8
Remove unused option in BaseCellCalling.step1.py

#17 nrockweiler opened 11 months ago
0
Fix basecallingstep1

#16 kane9530 opened 11 months ago
0
how to convert to the regular VCF file genotype such as 0/0 0/1 1/1

#15 linfanxiao closed 8 months ago
1
Warning for R package installation

#14 gangcai closed 11 months ago
3
Application to Smart-seq2

#13 LiQian-XC closed 11 months ago
2
Could this algorithm be used in Mouse data?

#12 RinconFer closed 10 months ago
6
SitesPerCell.py issue

#11 kane9530 closed 11 months ago
2
Fix VGAM==1.1-7 install

#10 anderswe opened 1 year ago
0