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questions
2
votes
3
replies
293
views
6 follow
How to summarize the expression of a gene when having expression data from different transcripts of that gene
rnaseq
expression
updated 6 weeks ago by
i.sudbery
16k • written 6 weeks ago by
jeni
▴ 90
0
votes
0
replies
234
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
VariantCalling
14 months ago by
jeni
▴ 90
10
votes
5
replies
4.6k
views
Remove supplementary alignments from a bam file
alignment
updated 2.0 years ago by
cianagalis
• 0 • written 2.9 years ago by
jeni
▴ 90
0
votes
1
reply
493
views
How to statistically determine if a mutation has an impact on expression individually for one patient
RNA-Seq
variant calling
2.2 years ago by
jeni
▴ 90
0
votes
3
replies
494
views
Correct number of detected variants by coverage
variant calling
2.3 years ago by
jeni
▴ 90
0
votes
3
replies
739
views
Differencial expression analysis between groups determined by two variables
expression
microarray
clustering
2.5 years ago by
jeni
▴ 90
3
votes
6
replies
1.1k
views
Does it make sense to transform expression data to zscore after performing RMA?
microarray
expression
updated 10 months ago by
kountaydwivedi
• 0 • written 2.5 years ago by
jeni
▴ 90
0
votes
0
replies
560
views
Is it right to use a low amount of bumphunter permutations?
methylation
microarray
DMR
2.5 years ago by
jeni
▴ 90
0
votes
0
replies
454
views
How to deal with SNPs and INDELs called in hypermutated regions?
variant calling
2.6 years ago by
jeni
▴ 90
0
votes
0
replies
469
views
Where to find a list of hypermutated regions for hg19 assembly?
variant calling
2.7 years ago by
jeni
▴ 90
2
votes
1
reply
742
views
How to know which genes are favouring or inactivating a pathway in a gene set enrichment analysis
enrichment analysis
updated 2.7 years ago by
Papyrus
★ 2.4k • written 2.7 years ago by
jeni
▴ 90
0
votes
0
replies
818
views
Reduce GRanges by different lengths of overlapping, deppending on each compared intervals
GRanges
2.8 years ago by
jeni
▴ 90
1
vote
3
replies
2.2k
views
HOMER hg19 not found in config.txt
HOMER
motif
finding
updated 19 months ago by
Sarah
• 0 • written 2.8 years ago by
jeni
▴ 90
3
votes
9
replies
950
views
Best practice to find regulatory motifs in a set of sequences
regulatory
motif
finding
updated 2.8 years ago by
Mensur Dlakic
★ 23k • written 2.8 years ago by
jeni
▴ 90
3
votes
3
replies
922
views
Best way to call differencially methylated positions taking into account results from both Beta and M values
methylation
updated 2.8 years ago by
Papyrus
★ 2.4k • written 2.8 years ago by
jeni
▴ 90
2
votes
5
replies
953
views
VEP is returning MOTIF_NAME values not recognised by Ensembl
snp
Ensembl
VEP
updated 2.8 years ago by
Michal @Ensembl
▴ 270 • written 2.8 years ago by
jeni
▴ 90
0
votes
0
replies
526
views
Download all positions where a motif exist from the genome browser
genome
2.8 years ago by
jeni
▴ 90
0
votes
6
replies
515
views
Pathways analysis taking into account the number of times a gene is present among several patients
snp
2.9 years ago by
jeni
▴ 90
2
votes
2
replies
965
views
Read genotype information with VariantAnnotation
SNP
R
vcf
Bioconductor
VariantAnnotation
updated 2.9 years ago by
benformatics
3.5k • written 2.9 years ago by
jeni
▴ 90
0
votes
2
replies
704
views
filter_vep not properly filtering
snp
updated 2.9 years ago by
Ram
38k • written 2.9 years ago by
jeni
▴ 90
5
votes
6
replies
2.4k
views
Parse VEP VCF with variantAnnotation
snp
R
2.9 years ago by
jeni
▴ 90
1
vote
4
replies
1.2k
views
Is it right to combine multiple runs downloaded from SRA?
next-gen
2.9 years ago by
jeni
▴ 90
0
votes
4
replies
482
views
How to remove reads supporting the same fragment that other reads support
Assembly
genome
3.0 years ago by
jeni
▴ 90
2
votes
6
replies
2.0k
views
Extract reads with insert size 0 from a bam file
alignment
updated 3.0 years ago by
Friederike
8.6k • written 3.0 years ago by
jeni
▴ 90
0
votes
5
replies
681
views
Transform genomic intervals to genomic positions in an R dataframe
R
3.0 years ago by
jeni
▴ 90
0
votes
1
reply
587
views
Plot per base coverage from regions coverage with R
R
updated 3.0 years ago by
lakhujanivijay
5.7k • written 3.0 years ago by
jeni
▴ 90
0
votes
2
replies
956
views
Minfi preprocessNoob vs preprocessQuantile normalization for Illumina EPIC array
R
Minfi
bioconductor
updated 3.3 years ago by
zx8754
11k • written 3.3 years ago by
jeni
▴ 90
0
votes
0
replies
743
views
Get IlluminaHumanMethylationEPICmanifest.bpm file
R
Bioconductor
updated 3.3 years ago by
zx8754
11k • written 3.3 years ago by
jeni
▴ 90
0
votes
0
replies
578
views
Get probe names from HTAFeatureSet expression data
R
3.3 years ago by
jeni
▴ 90
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