Showing : genomicalignments • reset
3
votes
2
replies
2.0k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 8.9 years ago by ★ 6.6k • written 8.9 years ago by ▴ 30
0
votes
1
reply
1.6k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 40
2
votes
2
replies
1.6k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 70
0
votes
4
replies
2.1k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
9.0 years ago mikko.arvas • 0
0
votes
1
reply
1.2k
views
genomicAlignments: fail to run readGAlignments example code
genomicAlignments
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 170
2
votes
4
replies
2.3k
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
9.0 years ago jma1991 ▴ 70
1
vote
2
replies
1.7k
views
How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
genomicalignments narrow mismatch
9.0 years ago Chao-Jen Wong ▴ 40
1
vote
3
replies
2.6k
views
GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
genomicalignments
updated 9.0 years ago by ★ 11k • written 9.1 years ago by ▴ 40
2
votes
6
replies
2.1k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
2
votes
7
replies
3.1k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
9.1 years ago lovro0 ▴ 10
3
votes
8
replies
1.9k
views
findSpliceOverlaps Buffer Error
GenomicAlignments findSpliceOverlaps
updated 9.1 years ago by 16k • written 9.2 years ago by ★ 1.6k
1
vote
2
replies
1.1k
views
in genomicAlignments, what="seq" doesn't work in readGAlignmentPairs ?
genomicalignments
9.2 years ago lovro0 ▴ 10
2
votes
2
replies
1.1k
views
Class for Storing Chimeric Reads
GenomicAlignments chimeric
updated 9.2 years ago by ★ 6.8k • written 9.2 years ago by ★ 1.6k
2
votes
2
replies
1.6k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 50
2
votes
1
reply
1.3k
views
RNAseq workflow exception with Rsamtools
rsamtools genomicalignments
updated 9.3 years ago by ★ 6.6k • written 9.3 years ago by ▴ 10
0
votes
5
replies
2.3k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
9.4 years ago philipp.wahle • 0
8
votes
3
replies
2.0k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 110
0
votes
1
reply
1.8k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 9.5 years ago by 16k • written 9.5 years ago by • 0
4
votes
2
replies
1.8k
views
readGAlignmentPairs not working correctly when reading a bam file by chunks
rsamtools genomicalignments genomicfiles
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 30
1
vote
2
replies
1.1k
views
slow granges in GAlignmentPairs
GenomicAlignments
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 20
1
vote
4
replies
1.9k
views
Issues installing GenomicAlignments
genomicalignments
9.7 years ago Radhouane Aniba ▴ 240
2
votes
1
reply
5.3k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 80
0
votes
2
replies
1.1k
views
queryLoc2refLoc not implemented?
GenomicAlignments
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 20
0
votes
2
replies
2.0k
views
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
1
vote
1
reply
1.9k
views
Different junction numbers from sashimi plot of Gviz package and summarizeJunctions() of GenomicAlignments package
gviz genomicalignments
updated 10.0 years ago by ▴ 750 • written 10.0 years ago by • 0
0
votes
2
replies
1.8k
views
stackStringsFromBam with paired-end reads
stackStringsFromBam genomicalignments GenomicAlignments
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 90
1
vote
4
replies
2.6k
views
GenomicAlignments: counting transcripts versus counting genes
genomicalignments
updated 10.1 years ago by ★ 1.7k • written 10.1 years ago by • 0
0
votes
3
replies
3.6k
views
get trimmed sequences based on cigar string in genomic alignments
genomicalignments
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 90
5
votes
3
replies
1.5k
views
sequenceLayer memory/C code problem?
genomicalignments c gviz
updated 10.1 years ago by 16k • written 10.2 years ago by ★ 2.1k
2
votes
2
replies
1.9k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 10
5
votes
5
replies
5.0k
views
Error when reading bam file with duplicated header
rsamtools genomicalignments
updated 10.3 years ago by ▴ 10 • written 10.6 years ago by ▴ 20
1
vote
12
replies
4.9k
views
Problem with summarizeOverlaps function
genomicalignments read counting
10.4 years ago kgorczak ▴ 10
4
votes
5
replies
1.9k
views
readGAlignmentPairs slow in problematic region
genomicalignments
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by 43k
1
vote
3
replies
2.8k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.4 years ago by • 0 • written 10.9 years ago by • 0
2
votes
2
replies
3.1k
views
How to randomly sample BAM files
rsamtools genomicalignments genomicfiles
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 70
0
votes
13
replies
3.2k
views
readGAlignments + BamViews not working in BioC-Devel
genomicalignments rsamtools
10.5 years ago Arne Muller ▴ 20
8
votes
9
replies
6.9k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.5 years ago by • 0 • written 10.5 years ago by ★ 1.5k
4
votes
4
replies
2.3k
views
Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
genomicalignments deseq2 rnaseq
updated 10.5 years ago by ★ 6.8k • written 10.5 years ago by ▴ 230
1
vote
2
replies
2.5k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 90
4
votes
2
replies
1.9k
views
Slice of aligned sequences
bam granges genomicalignments
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 10
4
votes
4
replies
3.1k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 10.6 years ago by ▴ 180 • written 10.6 years ago by • 0
6
votes
8
replies
3.1k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 10.6 years ago by ★ 8.2k • written 10.6 years ago by • 0
11
votes
8
replies
5.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 10
3
votes
4
replies
1.9k
views
problem with getting a subset of alignments mapping to a GRange using readGAlignmentsFromBam
genomicalignments scanbamparam
updated 10.8 years ago by 68k • written 10.8 years ago by ▴ 10
0
votes
5
replies
1.9k
views
Graphing coverage() results
ggbio genomicalignments bam
10.9 years ago gen ▴ 30
3
votes
12
replies
3.2k
views
performance issues when using readGAlignmentPairs with a ‘which’ argument
genomicalignments
10.9 years ago Leonard Goldstein ▴ 90
0
votes
2
replies
2.0k
views
GenomicAlignments update for R version 3.1.2
genomicalignments
updated 11.0 years ago by • 0 • written 11.1 years ago by • 0
6
votes
14
replies
7.4k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 11.0 years ago by 53k • written 11.0 years ago by • 0
0
votes
3
replies
2.9k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 11.2 years ago by ★ 8.2k • written 11.2 years ago by ▴ 20
6
votes
11
replies
4.5k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 11.2 years ago by ▴ 180 • written 11.2 years ago by ▴ 40
106 results • Page 2 of 3
Recent ...
Replies
Answer: GSEA in R/Bioconductor course by surferssubway743 • 0
[Subway Surfers][1] is a fun and challenging endless runner game that will keep you on the edge of your seat. At the beginning of the game,…
Answer: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by surferssubway743 • 0
Several new characters, a galaxy map, and several space tunnel exploration methods are all part of [Run 3][1], the third installment in the…
Answer: ChAMP pipeline error (champ.import) by surferssubway743 • 0
[Geometry Dash Subzero][1] has a harder difficulty level with more enemies and more involved gameplay that needs lightning-fast reflexes an…
Comment: DECIPHER DesignProbes unable to design FISH-probes by waveappeal • 0
@[Geometry][1] Snapchat truly remains a popular app that fosters connection among people. Follow and stay updated to build and develop a su…
Comment: Guitar R package requires update due to dependency GenomicFeatures by crystalswing • 0
@[Slope Free][1] I'm impressed with your referrals for effectively fixing these issues. I'll be following up and potentially gathering more…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Teacher to Michael Love 43k
Popular Question to lianov • 0
Locations • All
Spain, 1 hour ago
The city by the bay, 2 hours ago
usa, 3 hours ago
United States, 3 hours ago
Paraguay, 3 hours ago
Traffic: 1650 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6