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aeeckhou
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shallowHRD
This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
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Error in finding the 1st threshold
#22
DolapoA
closed
1 month ago
4
shallowHRD_hg19_1.13_QDNAseq_no_chrX.R zone 21 position inaccuracy
#21
GGanakin
closed
3 months ago
1
shallowHRDv2
#20
ToonRosseel
closed
3 months ago
1
cMAD question
#19
carolinehey
closed
5 months ago
2
Chromosomal arm addition is fundamentally incorrect
#18
lbeltrame
opened
8 months ago
0
Why are some LGAs not registered
#17
carolinehey
closed
9 months ago
1
Filename issues and continue on error
#16
menzel
closed
9 months ago
3
Help to identify this error.
#15
carolinehey
closed
9 months ago
7
where to find the newest shallowHRD_hg38 script?
#14
carolinehey
closed
9 months ago
2
Logic error in merging segments
#13
lbeltrame
closed
11 months ago
1
Comment doesn't seem to match the code when merging small segments with larger ones
#12
lbeltrame
closed
11 months ago
2
freezing after starting script
#11
EtieM
closed
1 year ago
4
Why are most of the calculations done twice?
#10
lbeltrame
closed
1 year ago
4
new version on hg38
#9
laurie-tonon
closed
1 year ago
3
how to use it to detect genome homologous recombination in non-human resequsing data?
#8
Yixiangzhang1996
closed
1 year ago
1
different LGA results between versions
#7
danyuewang
closed
1 year ago
1
Variable error in QDNA_from_bam_no_chrX.R
#6
DucoG
closed
1 year ago
1
Frozen calculation of a sample
#5
Fponelle
closed
2 years ago
0
Error or typo in the script
#4
zhqingit
closed
2 years ago
1
X = X[which(X[,6] > ((quantile(X[,6])[[4]] - quantile(X[,6])[[2]])/2)),]
#3
axiba053
closed
3 years ago
4
full command to run shallowHRD using ichorCNA output file
#2
asaki1986
closed
3 years ago
6
Readme edition v1 05/09/2016
#1
aeeckhou
closed
4 years ago
0