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637
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rtracklayer import only subset of ranges
rtracklayer
updated 22 months ago by 3.9k • written 22 months ago by ▴ 90
1
vote
1
reply
960
views
Average coverage between multiple samples
GenomicRanges
updated 3.5 years ago by ★ 11k • written 3.5 years ago by ▴ 90
0
votes
2
replies
1.1k
views
Gviz vertical text labels
Gviz
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 90
0
votes
1
reply
4.7k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.9 years ago by 66k • written 3.9 years ago by ▴ 90
0
votes
3
replies
989
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.5 years ago by ★ 11k • written 4.5 years ago by ▴ 90
2
votes
1
reply
701
views
Small differences in limma with and without contrast matrix
limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 90
2
votes
2
replies
763
views
Normalize for changes in one direction
limma voom rnaseq
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 90
0
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1
reply
1.1k
views
Comment: C: Non-used samples changing number of significant genes in limma
6.7 years ago Jake ▴ 90
0
votes
3
replies
1.1k
views
Non-used samples changing number of significant genes in limma
limma voom
6.7 years ago Jake ▴ 90
7
votes
4
replies
3.0k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 7.0 years ago by • 0 • written 8.6 years ago by ▴ 90
2
votes
1
reply
987
views
pintersect and psetdiff changed behavior
genomicranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 90
6
votes
6
replies
2.6k
views
Ribosome profiling analysis in DEseq2/limma
deseq2 limma
written 9.2 years ago by ▴ 90
0
votes
0
replies
1.4k
views
RNA-Seq metagene coverage
coverage
8.0 years ago Jake ▴ 90
4
votes
6
replies
1.4k
views
Differential expression across gene features
limma deseq2 differential gene expression
written 8.2 years ago by ▴ 90
6
votes
4
replies
4.3k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 8.0 years ago by 51k • written 8.0 years ago by ▴ 90
0
votes
0
replies
4.3k
views
Comment: C: RSEM expected counts to limma-voom
8.0 years ago Jake ▴ 90
0
votes
3
replies
1.3k
views
matchPWM on DNAStringSet rather than just one sequence?
biostrings
8.1 years ago Jake ▴ 90
0
votes
1
reply
1.3k
views
Answer: A: matchPWM on DNAStringSet rather than just one sequence?
8.1 years ago Jake ▴ 90
2
votes
10
replies
1.9k
views
Reorder exons on negative strand in GRanges list
genomicranges
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 90
0
votes
2
replies
1.4k
views
Comment: C: Differential expression across gene features
8.2 years ago Jake ▴ 90
4
votes
2
replies
3.2k
views
limma-voom for miRNA seq
limma voom
updated 8.4 years ago by 51k • written 8.4 years ago by ▴ 90
0
votes
1
reply
1.2k
views
Comment: C: Write multiple UTRs for a gene to a fasta file
8.4 years ago Jake ▴ 90
4
votes
5
replies
1.2k
views
Write multiple UTRs for a gene to a fasta file
genomicranges genomicfeatures
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 90
3
votes
1
reply
2.0k
views
does pca assume no heteroscedasticity?
deseq2 pca
updated 8.4 years ago by 42k • written 8.4 years ago by ▴ 90
0
votes
1
reply
2.8k
views
Comment: C: get trimmed sequences based on cigar string in genomic alignments
8.6 years ago Jake ▴ 90
0
votes
3
replies
2.8k
views
get trimmed sequences based on cigar string in genomic alignments
genomicalignments
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 90
0
votes
1
reply
1.9k
views
Comment: C: issue renaming seqnames in genomic ranges
8.6 years ago Jake ▴ 90
1
vote
3
replies
1.9k
views
issue renaming seqnames in genomic ranges
genomicranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 90
3
votes
1
reply
3.8k
views
Best way to convert ensembl id to mgi?
annotation biomart
updated 8.7 years ago by 66k • written 8.7 years ago by ▴ 90
0
votes
1
reply
1.8k
views
Comment: C: remove set number of nucleotides from each gene's cds region in GRangesList
8.8 years ago Jake ▴ 90
0
votes
1
reply
1.8k
views
Comment: C: remove set number of nucleotides from each gene's cds region in GRangesList
8.8 years ago Jake ▴ 90
0
votes
1
reply
1.8k
views
Comment: C: remove set number of nucleotides from each gene's cds region in GRangesList
8.8 years ago Jake ▴ 90
0
votes
1
reply
1.8k
views
Comment: C: remove set number of nucleotides from each gene's cds region in GRangesList
8.8 years ago Jake ▴ 90
0
votes
0
replies
1.8k
views
Comment: C: remove set number of nucleotides from each gene's cds region in GRangesList
8.8 years ago Jake ▴ 90
2
votes
12
replies
1.8k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 90
3
votes
3
replies
2.2k
views
ribosome profiling analysis with different dispersions
deseq2 linear model ribosome profiling stats
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 90
0
votes
1
reply
6.3k
views
Comment: C: rtracklayer export GRangesList as gtf and change attributes
9.0 years ago Jake ▴ 90
2
votes
4
replies
6.3k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.0 years ago by • 0 • written 9.0 years ago by ▴ 90
0
votes
1
reply
6.3k
views
Answer: A: SummarizeOverlaps in R
9.0 years ago Jake ▴ 90
0
votes
1
reply
4.2k
views
Comment: C: coverage over specific GenomicRanges
9.0 years ago Jake ▴ 90
0
votes
1
reply
2.1k
views
Comment: C: Check DESeq2 contrasts for exon vs intron changes
9.0 years ago Jake ▴ 90
0
votes
1
reply
2.1k
views
Comment: C: Check DESeq2 contrasts for exon vs intron changes
9.0 years ago Jake ▴ 90
1
vote
2
replies
2.0k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 90
0
votes
1
reply
4.2k
views
Comment: C: coverage over specific GenomicRanges
9.0 years ago Jake ▴ 90
2
votes
7
replies
4.2k
views
coverage over specific GenomicRanges
genomicranges
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 90
0
votes
1
reply
2.1k
views
Comment: C: Check DESeq2 contrasts for exon vs intron changes
9.0 years ago Jake ▴ 90
1
vote
1
reply
3.4k
views
bedtools like subtract in genomic ranges?
genomicranges
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 90
2
votes
9
replies
2.1k
views
Check DESeq2 contrasts for exon vs intron changes
deseq2 linear model
updated 9.0 years ago by 42k • written 9.0 years ago by ▴ 90
0
votes
1
reply
1.2k
views
dual core vs quad core, ram for seq analysis
ram dualcore quadcore
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 90
1
vote
1
reply
1.3k
views
Controlling for/removing batch effect
deseq2 sva
updated 9.1 years ago by 66k • written 9.1 years ago by ▴ 90
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