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2
votes
3
replies
765
views
6 follow
How to summarize the expression of a gene when having expression data from different transcripts of that gene
rnaseq expression
updated 15 months ago by 19k • written 15 months ago by ▴ 90
0
votes
0
replies
387
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
Variant-Calling
updated 7 weeks ago by 43k • written 2.3 years ago by ▴ 90
0
votes
1
reply
4.6k
views
Comment: Comment: MAGERI: a software tool for calling rare variants and detecting circulating tumo
3.0 years ago by jeni ▴ 90
11
votes
5
replies
7.3k
views
Remove supplementary alignments from a bam file
alignment
updated 3.2 years ago by • 0 • written 4.1 years ago by ▴ 90
0
votes
1
reply
643
views
How to statistically determine if a mutation has an impact on expression individually for one patient
RNA-Seq variant calling
3.3 years ago by jeni ▴ 90
0
votes
1
reply
720
views
Comment: C: Correct number of detected variants by coverage
3.5 years ago by jeni ▴ 90
0
votes
3
replies
720
views
Correct number of detected variants by coverage
variant calling
3.5 years ago by jeni ▴ 90
0
votes
0
replies
1.0k
views
Comment: C: Differencial expression analysis between groups determined by two variables
3.6 years ago by jeni ▴ 90
0
votes
3
replies
1.0k
views
Differencial expression analysis between groups determined by two variables
expression microarray clustering
3.6 years ago by jeni ▴ 90
0
votes
1
reply
1.6k
views
Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
3.6 years ago by jeni ▴ 90
0
votes
1
reply
1.6k
views
Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
3.6 years ago by jeni ▴ 90
3
votes
6
replies
1.6k
views
Does it make sense to transform expression data to zscore after performing RMA?
microarray expression
updated 2.0 years ago by • 0 • written 3.6 years ago by ▴ 90
0
votes
0
replies
698
views
Is it right to use a low amount of bumphunter permutations?
methylation microarray DMR
3.6 years ago by jeni ▴ 90
0
votes
1
reply
2.9k
views
Comment: C: HOMER hg19 not found in config.txt
3.6 years ago by jeni ▴ 90
0
votes
0
replies
569
views
How to deal with SNPs and INDELs called in hypermutated regions?
variant calling
3.8 years ago by jeni ▴ 90
0
votes
0
replies
610
views
Where to find a list of hypermutated regions for hg19 assembly?
variant calling
3.8 years ago by jeni ▴ 90
2
votes
1
reply
999
views
How to know which genes are favouring or inactivating a pathway in a gene set enrichment analysis
enrichment analysis
updated 3.8 years ago by ★ 2.9k • written 3.8 years ago by ▴ 90
0
votes
0
replies
1.0k
views
Reduce GRanges by different lengths of overlapping, deppending on each compared intervals
GRanges
3.9 years ago by jeni ▴ 90
1
vote
3
replies
2.9k
views
HOMER hg19 not found in config.txt
HOMER motif finding
updated 2.8 years ago by • 0 • written 3.9 years ago by ▴ 90
0
votes
0
replies
1.4k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.9 years ago by jeni ▴ 90
0
votes
1
reply
1.4k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.9 years ago by jeni ▴ 90
0
votes
1
reply
1.4k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.9 years ago by jeni ▴ 90
3
votes
9
replies
1.4k
views
Best practice to find regulatory motifs in a set of sequences
regulatory motif finding
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 90
0
votes
1
reply
1.4k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.9 years ago by jeni ▴ 90
0
votes
1
reply
1.2k
views
Comment: C: Best way to call differencially methylated positions taking into account results
3.9 years ago by jeni ▴ 90
3
votes
3
replies
1.2k
views
Best way to call differencially methylated positions taking into account results from both Beta and M values
methylation
updated 3.9 years ago by ★ 2.9k • written 3.9 years ago by ▴ 90
0
votes
1
reply
10k
views
Comment: C: Beta-values, M-values and thresholds on effect size
3.9 years ago by jeni ▴ 90
2
votes
5
replies
1.3k
views
VEP is returning MOTIF_NAME values not recognised by Ensembl
snp Ensembl VEP
updated 3.9 years ago by ▴ 270 • written 4.0 years ago by ▴ 90
0
votes
0
replies
788
views
Download all positions where a motif exist from the genome browser
genome
3.9 years ago by jeni ▴ 90
0
votes
1
reply
1.3k
views
Comment: C: VEP is returning MOTIF_NAME values not recognised by Ensembl
4.0 years ago by jeni ▴ 90
0
votes
0
replies
759
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
4.0 years ago by jeni ▴ 90
0
votes
1
reply
759
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
4.0 years ago by jeni ▴ 90
0
votes
1
reply
759
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
4.0 years ago by jeni ▴ 90
0
votes
6
replies
759
views
Pathways analysis taking into account the number of times a gene is present among several patients
snp
4.0 years ago by jeni ▴ 90
0
votes
0
replies
931
views
Comment: C: filter_vep not properly filtering
4.0 years ago by jeni ▴ 90
2
votes
2
replies
1.3k
views
Read genotype information with VariantAnnotation
SNP R vcf Bioconductor VariantAnnotation
updated 4.0 years ago by 3.9k • written 4.0 years ago by ▴ 90
0
votes
2
replies
931
views
filter_vep not properly filtering
snp
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 90
0
votes
0
replies
3.3k
views
Comment: C: Parse VEP VCF with variantAnnotation
4.1 years ago by jeni ▴ 90
5
votes
6
replies
3.3k
views
Parse VEP VCF with variantAnnotation
snp R
4.1 years ago by jeni ▴ 90
0
votes
0
replies
3.3k
views
Comment: C: Parse VEP VCF with variantAnnotation
4.1 years ago by jeni ▴ 90
0
votes
1
reply
1.5k
views
Comment: C: Is it right to combine multiple runs downloaded from SRA?
4.1 years ago by jeni ▴ 90
1
vote
4
replies
1.5k
views
Is it right to combine multiple runs downloaded from SRA?
next-gen
4.1 years ago by jeni ▴ 90
0
votes
4
replies
685
views
How to remove reads supporting the same fragment that other reads support
Assembly genome
4.1 years ago by jeni ▴ 90
0
votes
0
replies
685
views
Comment: C: How to remove reads supporting the same fragment that other reads support
4.1 years ago by jeni ▴ 90
2
votes
6
replies
3.0k
views
Extract reads with insert size 0 from a bam file
alignment
updated 4.1 years ago by 8.9k • written 4.1 years ago by ▴ 90
0
votes
0
replies
3.0k
views
Comment: C: Extract reads with insert size 0 from a bam file
4.1 years ago by jeni ▴ 90
0
votes
1
reply
3.0k
views
Comment: C: Extract reads with insert size 0 from a bam file
4.1 years ago by jeni ▴ 90
0
votes
0
replies
948
views
Comment: C: Transform genomic intervals to genomic positions in an R dataframe
updated 4.1 years ago by 88k • written 4.2 years ago by ▴ 90
0
votes
1
reply
948
views
Comment: C: Transform genomic intervals to genomic positions in an R dataframe
4.2 years ago by jeni ▴ 90
0
votes
5
replies
948
views
Transform genomic intervals to genomic positions in an R dataframe
R
4.2 years ago by jeni ▴ 90
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