issues
search
ChristofferFlensburg
/
superFreq
Analysis pipeline for cancer sequencing data
MIT License
110
stars
33
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
No reads in samples
#127
mlegarreta00
opened
2 months ago
1
Plot interpretation
#126
Teezi
closed
2 months ago
2
Columns of CNAbyGene.tsv file
#125
mlegarreta00
closed
2 months ago
1
error: Flagging SNPs that are in noisy regions. New flags by sample:Killed
#124
Teezi
closed
2 months ago
8
featureCounts setting: `Count read pairs : no`
#123
Teezi
closed
5 months ago
2
Can reference normal files include the same bam file used for input?
#122
mlegarreta00
closed
5 months ago
1
Concermong about Normal reference
#121
km-2021
closed
2 months ago
1
SuperFreq cannot find varscan command
#120
avivneuronvision
closed
2 months ago
1
Output graph optimization
#119
nerea-bilbao
closed
2 months ago
1
Retrieve ploidy fit value / - How to compute Chromosome Instability (CIN) Index - Fraction Genome Altered (FGA) ?
#118
ZheFrench
closed
2 months ago
1
Ok, I had a closer look at the latest Rsubread version, and they have indeed changed syntax for how to tell it to to count raw reads (not fragments) in PE samples. And that is most likely they cause of the bug. I made a change to superFreq that reads out the Rsubread version and does the appropriate call. Running tests and will push online, but will (hopefully) be next week. You can either backdate Rsubread if you're in a hurry, or wait for me to finish the testing and push changes online.
#117
duanshumeng
closed
11 months ago
2
VariantAnnotation step failing in v1.5.1
#116
samleenz
closed
11 months ago
2
Recommendations to process large cohort of normal/tumoral RNASEQ pair
#115
ZheFrench
closed
1 year ago
7
Some variants are missing in river.tsv
#114
pigyun906
closed
2 months ago
1
Failed annotation - "data set ‘entrez2symbol_hs’ not found"
#113
gbss2
closed
1 year ago
3
Question about superFreq copy number call output
#112
km-2021
closed
2 months ago
1
Is it possible to track which subclones contain a specific genetic mutation in a superFreq riverplot?
#111
km-2021
closed
2 months ago
1
Issue connecting to GitLab server
#110
km-2021
closed
2 months ago
10
WriteXLS error in large cohort analysis
#109
leap-ahead225
closed
1 year ago
8
RNA mode
#108
km-2021
closed
1 year ago
1
RNA mode
#107
km-2021
closed
1 year ago
1
About reference
#106
km-2021
closed
1 year ago
1
error in RNA mode
#105
km-2021
closed
1 year ago
1
SuperFreq result interpretation for amplificaiton events from RNA-Seq
#104
akshaya1296
closed
1 year ago
4
Error during running the recent version with #94
#103
pigyun906
closed
1 year ago
2
findCorrespondingNormal returns missing value
#102
hosseinvk
closed
1 year ago
5
Tracking back the sequences of the clones
#101
maheshworpaudel5001
closed
2 months ago
1
Could not parse the "#CHROM.." line
#100
maheshworpaudel5001
closed
1 year ago
6
Successfully assigned alignments 0 error
#99
maheshworpaudel5001
closed
1 year ago
4
X11 display error
#98
maheshworpaudel5001
closed
1 year ago
5
polyclonal or monoconal model from river plot
#97
ada6090
closed
1 year ago
9
Mv flag is too much (?)
#96
underbais
closed
2 months ago
5
Update getStories.R
#95
mattpito
opened
1 year ago
0
Error during running the recent version
#94
sohyoung27
closed
2 months ago
11
Input for ClonEvol
#93
pigyun906
closed
1 year ago
1
Plotting only "LFC vs normals" or "SNP MAF" graph from the CNV figure
#92
ElsaMichelle
closed
2 months ago
1
Capture regions read
#91
arpanda
closed
2 years ago
4
Error log is not clear !
#90
arpanda
closed
2 years ago
4
wget download is not working
#89
arpanda
closed
2 years ago
5
Understanding columns in the CNA segment output file
#88
jsha129
closed
2 months ago
1
CNV calls in Chr X and Y
#87
mike8115
closed
2 months ago
3
CNA calls in the output
#86
zozcan89
closed
2 months ago
1
Error in base::basename(path, ...) : a character vector argument expected
#85
deb0612
closed
2 months ago
1
superFreq forces R and plots to be created on same path as control samples
#84
emauryg
closed
2 years ago
22
New variants excel file
#83
UmairAhmadKhan97
closed
3 years ago
2
Concatenating metadata for runSummaryPostAnalysis
#82
UmairAhmadKhan97
closed
3 years ago
2
Explanation of fields in rivers files
#81
kmavrommatis
closed
2 months ago
1
Hi Christoffer, I was wondering how to get B allele frequency from the characterized SNPs
#80
YuehuiZ
closed
3 years ago
2
Memory Issues
#79
UmairAhmadKhan97
closed
3 years ago
11
Error in featureCounts
#78
UmairAhmadKhan97
closed
3 years ago
3
Next