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2
votes
3
replies
351
views
6 follow
How to summarize the expression of a gene when having expression data from different transcripts of that gene
rnaseq expression
updated 4 months ago by 17k • written 4 months ago by ▴ 90
0
votes
0
replies
250
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
VariantCalling
17 months ago by jeni ▴ 90
0
votes
0
replies
4.1k
views
Comment: Comment: MAGERI: a software tool for calling rare variants and detecting circulating tumo
2.0 years ago by jeni ▴ 90
10
votes
5
replies
5.1k
views
Remove supplementary alignments from a bam file
alignment
updated 2.2 years ago by • 0 • written 3.2 years ago by ▴ 90
0
votes
1
reply
507
views
How to statistically determine if a mutation has an impact on expression individually for one patient
RNA-Seq variant calling
2.4 years ago by jeni ▴ 90
0
votes
1
reply
514
views
Comment: C: Correct number of detected variants by coverage
2.6 years ago by jeni ▴ 90
0
votes
3
replies
514
views
Correct number of detected variants by coverage
variant calling
2.6 years ago by jeni ▴ 90
0
votes
0
replies
784
views
Comment: C: Differencial expression analysis between groups determined by two variables
2.7 years ago by jeni ▴ 90
0
votes
3
replies
784
views
Differencial expression analysis between groups determined by two variables
expression microarray clustering
2.7 years ago by jeni ▴ 90
0
votes
1
reply
1.2k
views
Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
2.7 years ago by jeni ▴ 90
0
votes
1
reply
1.2k
views
Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
2.7 years ago by jeni ▴ 90
3
votes
6
replies
1.2k
views
Does it make sense to transform expression data to zscore after performing RMA?
microarray expression
updated 13 months ago by • 0 • written 2.7 years ago by ▴ 90
0
votes
0
replies
580
views
Is it right to use a low amount of bumphunter permutations?
methylation microarray DMR
2.7 years ago by jeni ▴ 90
0
votes
1
reply
2.3k
views
Comment: C: HOMER hg19 not found in config.txt
2.7 years ago by jeni ▴ 90
0
votes
0
replies
469
views
How to deal with SNPs and INDELs called in hypermutated regions?
variant calling
2.8 years ago by jeni ▴ 90
0
votes
0
replies
484
views
Where to find a list of hypermutated regions for hg19 assembly?
variant calling
2.9 years ago by jeni ▴ 90
2
votes
1
reply
776
views
How to know which genes are favouring or inactivating a pathway in a gene set enrichment analysis
enrichment analysis
updated 2.9 years ago by ★ 2.5k • written 2.9 years ago by ▴ 90
0
votes
0
replies
858
views
Reduce GRanges by different lengths of overlapping, deppending on each compared intervals
GRanges
3.0 years ago by jeni ▴ 90
1
vote
3
replies
2.3k
views
HOMER hg19 not found in config.txt
HOMER motif finding
updated 22 months ago by • 0 • written 3.0 years ago by ▴ 90
0
votes
0
replies
1.0k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.0 years ago by jeni ▴ 90
0
votes
1
reply
1.0k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.0 years ago by jeni ▴ 90
0
votes
1
reply
1.0k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.0 years ago by jeni ▴ 90
3
votes
9
replies
1.0k
views
Best practice to find regulatory motifs in a set of sequences
regulatory motif finding
updated 3.0 years ago by ★ 23k • written 3.0 years ago by ▴ 90
0
votes
1
reply
1.0k
views
Comment: C: Best practice to find regulatory motifs in a set of sequences
3.0 years ago by jeni ▴ 90
0
votes
1
reply
965
views
Comment: C: Best way to call differencially methylated positions taking into account results
3.0 years ago by jeni ▴ 90
3
votes
3
replies
965
views
Best way to call differencially methylated positions taking into account results from both Beta and M values
methylation
updated 3.0 years ago by ★ 2.5k • written 3.0 years ago by ▴ 90
0
votes
1
reply
9.6k
views
Comment: C: Beta-values, M-values and thresholds on effect size
3.0 years ago by jeni ▴ 90
2
votes
5
replies
1.0k
views
VEP is returning MOTIF_NAME values not recognised by Ensembl
snp Ensembl VEP
updated 3.0 years ago by ▴ 270 • written 3.0 years ago by ▴ 90
0
votes
0
replies
556
views
Download all positions where a motif exist from the genome browser
genome
3.0 years ago by jeni ▴ 90
0
votes
1
reply
1.0k
views
Comment: C: VEP is returning MOTIF_NAME values not recognised by Ensembl
3.0 years ago by jeni ▴ 90
0
votes
0
replies
539
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
3.1 years ago by jeni ▴ 90
0
votes
1
reply
539
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
3.1 years ago by jeni ▴ 90
0
votes
1
reply
539
views
Comment: C: Pathways analysis taking into account the number of times a gene is present amon
3.1 years ago by jeni ▴ 90
0
votes
6
replies
539
views
Pathways analysis taking into account the number of times a gene is present among several patients
snp
3.1 years ago by jeni ▴ 90
0
votes
0
replies
740
views
Comment: C: filter_vep not properly filtering
3.1 years ago by jeni ▴ 90
2
votes
2
replies
1.0k
views
Read genotype information with VariantAnnotation
SNP R vcf Bioconductor VariantAnnotation
updated 3.1 years ago by 3.6k • written 3.1 years ago by ▴ 90
0
votes
2
replies
740
views
filter_vep not properly filtering
snp
updated 3.1 years ago by 39k • written 3.1 years ago by ▴ 90
0
votes
0
replies
2.6k
views
Comment: C: Parse VEP VCF with variantAnnotation
3.1 years ago by jeni ▴ 90
5
votes
6
replies
2.6k
views
Parse VEP VCF with variantAnnotation
snp R
3.1 years ago by jeni ▴ 90
0
votes
0
replies
2.6k
views
Comment: C: Parse VEP VCF with variantAnnotation
3.1 years ago by jeni ▴ 90
0
votes
1
reply
1.3k
views
Comment: C: Is it right to combine multiple runs downloaded from SRA?
3.1 years ago by jeni ▴ 90
1
vote
4
replies
1.3k
views
Is it right to combine multiple runs downloaded from SRA?
next-gen
3.1 years ago by jeni ▴ 90
0
votes
4
replies
507
views
How to remove reads supporting the same fragment that other reads support
Assembly genome
3.2 years ago by jeni ▴ 90
0
votes
0
replies
507
views
Comment: C: How to remove reads supporting the same fragment that other reads support
3.2 years ago by jeni ▴ 90
2
votes
6
replies
2.2k
views
Extract reads with insert size 0 from a bam file
alignment
updated 3.2 years ago by 8.7k • written 3.2 years ago by ▴ 90
0
votes
0
replies
2.2k
views
Comment: C: Extract reads with insert size 0 from a bam file
3.2 years ago by jeni ▴ 90
0
votes
1
reply
2.2k
views
Comment: C: Extract reads with insert size 0 from a bam file
3.2 years ago by jeni ▴ 90
0
votes
0
replies
722
views
Comment: C: Transform genomic intervals to genomic positions in an R dataframe
updated 3.2 years ago by 85k • written 3.2 years ago by ▴ 90
0
votes
1
reply
722
views
Comment: C: Transform genomic intervals to genomic positions in an R dataframe
3.2 years ago by jeni ▴ 90
0
votes
5
replies
722
views
Transform genomic intervals to genomic positions in an R dataframe
R
3.2 years ago by jeni ▴ 90
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