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Rsamtools
•
reset
0
votes
11
replies
2.1k
views
Rsubread/Rsamtools mappings outside of chromosome ranges
PROcess
Rsamtools
Rsubread
TCC
PROcess
Rsamtools
Rsubread
TCC
12.2 years ago
Thomas Girke
★ 1.7k
0
votes
13
replies
2.3k
views
readGAlignments + BamViews not working in BioC-Devel
genomicalignments
rsamtools
8.8 years ago
Arne Muller
▴ 20
3
votes
12
replies
2.4k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools
cn.mops
installation
9.0 years ago
Spollen, William G.
▴ 30
1
vote
4
replies
2.2k
views
How to find the end position of a read?
rsamtools
alignment
cigar
6.8 years ago
Frocha
▴ 20
4
votes
4
replies
2.4k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup
rsamtools
bam
genomicalignments
updated 8.9 years ago by
Nathaniel Hayden
▴ 180 • written 8.9 years ago by
Sam Buckberry
• 0
2
votes
4
replies
1.5k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Christopher
• 0
0
votes
4
replies
1.3k
views
pileup function not found (Rsamtools)
rsamtools
pileup
7.6 years ago
oscar puig
• 0
6
votes
5
replies
3.4k
views
Extracting Sequences from Fasta Files with Rsamtools
Rsamtools
updated 3.5 years ago by
Martin Morgan
25k • written 3.9 years ago by
jlee
▴ 20
0
votes
5
replies
1.2k
views
Rsamtools from biocLite using R-devel
Rsamtools
Rsamtools
updated 13.5 years ago by
Paul Leo
▴ 970 • written 13.5 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
6
replies
2.2k
views
Rsamtools installation
Rsamtools
Rsamtools
updated 12.5 years ago by
James W. MacDonald
65k • written 12.5 years ago by
John Coulthard
▴ 170
0
votes
2
replies
1.1k
views
Rsamtools ScanFA error
rsamtools
6.4 years ago
andreag1987
• 0
0
votes
4
replies
1.5k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 12.3 years ago by
davide risso
▴ 950 • written 12.3 years ago by
rcaloger
▴ 500
0
votes
7
replies
2.8k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation
PROcess
Rsamtools
VariantAnnotation
VariantAnnotation
PROcess
Rsamtools
updated 11.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.0 years ago by
UBod
▴ 290
5
votes
9
replies
2.2k
views
Reading alignments above a mapq threshold from BAM files
rsamtools
bam
updated 8.8 years ago by
Martin Morgan
25k • written 8.8 years ago by
Johannes Rainer
★ 2.0k
9
votes
32
replies
6.0k
views
Rsamtools v 1.99.6 installation error
Rsamtools
BiocManager
R 3.6
ubuntu
updated 5.0 years ago by
Hervé Pagès
16k • written 5.0 years ago by
kubovcij
• 0
1
vote
2
replies
1.7k
views
scanBam with ScanBamParam argument which specified ignores yieldSize. Intentionally?
scanbam
scanbamparam
rsamtools
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
Johannes Rainer
★ 2.0k
8
votes
3
replies
1.4k
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
rubi
▴ 110
1
vote
2
replies
1.3k
views
Rsamtools and dbnsfp
bioconductor
rsamtools
annotation
variantannotation
8.8 years ago
jhomsy
• 0
5
votes
15
replies
1.7k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 4.6 years ago by
Hervé Pagès
16k • written 4.6 years ago by
Gordon Smyth
50k
0
votes
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis
rsamtools
shortread
biostrings
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
travis.m.couture
• 0
5
votes
6
replies
2.3k
views
extracting Allele Read Counts
rsamtools
vcf
7.1 years ago
Bogdan
▴ 670
3
votes
2
replies
2.0k
views
Rsamtools use for R version 3.4.1
rsamtools
package installation
samtools
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
rbronste
▴ 60
0
votes
6
replies
1.7k
views
Problem installing Rsamtools
Rsamtools
Rsamtools
12.6 years ago
Kathryn Iverson
▴ 30
0
votes
3
replies
1.4k
views
Rsamtools installation
GO
Rsamtools
GO
Rsamtools
updated 12.1 years ago by
Martin Morgan
25k • written 12.1 years ago by
Bruce Hayward
▴ 40
0
votes
4
replies
3.8k
views
reading BAM files
Rsamtools
Rsamtools
updated 11.4 years ago by
James W. MacDonald
65k • written 11.4 years ago by
Hermann Norpois
▴ 110
1
vote
2
replies
2.2k
views
Processing bam files by read group
rsamtools
read group
bam
updated 9.3 years ago by
Nathaniel Hayden
▴ 180 • written 9.5 years ago by
Thomas Sandmann
▴ 90
0
votes
2
replies
1.2k
views
error from rsamtools on 1000 genomes
Cancer
HapMap
Rsamtools
genomes
Cancer
HapMap
Rsamtools
genomes
updated 13.8 years ago by
Martin Morgan
25k • written 13.8 years ago by
Sergii Ivakhno
▴ 100
2
votes
4
replies
2.9k
views
getSeq{BSgenome} error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome
rsamtools
8.3 years ago
komal.rathi
▴ 120
0
votes
6
replies
2.0k
views
Advice on reading big BED/BAM and ChIP-seq quality control
GO
rtracklayer
Rsamtools
GO
rtracklayer
Rsamtools
updated 11.0 years ago by
Michael Stadler
▴ 350 • written 11.0 years ago by
Hari Easwaran
▴ 240
4
votes
5
replies
2.3k
views
scanBam on BamSampler supposed to be fast?
rsamtools
bam
updated 9.3 years ago by
Martin Morgan
25k • written 9.3 years ago by
Johannes Rainer
★ 2.0k
0
votes
4
replies
1.1k
views
Is there support for tag type 'B' in Rsamtools?
rsamtools
software error
8.6 years ago
obanerjee
• 0
0
votes
6
replies
1.2k
views
wishlist for readGappedAlignments
GenomicRanges
Rsamtools
GenomicRanges
Rsamtools
updated 12.7 years ago by
Martin Morgan
25k • written 12.7 years ago by
Tengfei Yin
▴ 420
0
votes
2
replies
2.5k
views
How to access custom SAM tags (Rsamtools?)
Rsamtools
Rsamtools
updated 11.4 years ago by
delhomme@embl.de
★ 1.2k • written 11.4 years ago by
Kemal Akman
▴ 20
0
votes
2
replies
1.5k
views
[devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?
Coverage
Cancer
Rsamtools
Coverage
Cancer
Rsamtools
updated 11.3 years ago by
Renjie Tan
▴ 10 • written 11.3 years ago by
Martin Morgan
25k
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.2 years ago by
changxu.fan
▴ 20
0
votes
8
replies
3.6k
views
Rsamtools installation error
Rsamtools
Rsamtools
updated 11.8 years ago by
Dan Tenenbaum
★ 8.2k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
Rsamtools: Read a bam line by line
GO
Rsamtools
GO
Rsamtools
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
Alex Gutteridge
▴ 650
0
votes
1
reply
833
views
Accessing next gen sequence data remotely via biocondcutor
Sequencing
Rsamtools
Sequencing
Rsamtools
updated 13.4 years ago by
Martin Morgan
25k • written 13.4 years ago by
Ruppert Valentino
▴ 270
0
votes
1
reply
1.5k
views
Using readBAM function in segmentSeq
GO
Rsamtools
GO
Rsamtools
updated 11.8 years ago by
Thomas J Hardcastle
▴ 180 • written 11.8 years ago by
james perkins
▴ 300
0
votes
1
reply
955
views
Rsamtools: scanBamFlag bug?
Rsamtools
Rsamtools
updated 11.9 years ago by
Martin Morgan
25k • written 11.9 years ago by
Nuno Fonseca
▴ 10
0
votes
3
replies
1.1k
views
Rsamtools Error: vector of negative length
Rsamtools
Rsamtools
updated 13.5 years ago by
Martin Morgan
25k • written 13.5 years ago by
Christoph Bartenhagen
▴ 40
0
votes
1
reply
2.8k
views
Import Bam index (Rsamtools)
Proteomics
Rsamtools
Proteomics
Rsamtools
updated 12.1 years ago by
Martin Morgan
25k • written 12.1 years ago by
Francesco Mancuso
▴ 110
0
votes
2
replies
1.7k
views
Rsamtools installation error
ShortRead
Rsamtools
ShortRead
Rsamtools
updated 12.2 years ago by
Martin Morgan
25k • written 12.2 years ago by
Wolfgang Raffelsberger
▴ 60
0
votes
1
reply
849
views
[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage
Cancer
Rsamtools
Coverage
Cancer
Rsamtools
10.6 years ago
Hervé Pagès
16k
0
votes
1
reply
3.6k
views
writing BAM files from within R
convert
Rsamtools
convert
Rsamtools
updated 12.3 years ago by
Valerie Obenchain
★ 6.8k • written 12.3 years ago by
margherita mutarelli
▴ 10
0
votes
7
replies
1.1k
views
Rsamtools from biocLite using R-devel
Rsamtools
Rsamtools
updated 13.5 years ago by
Martin Morgan
25k • written 13.5 years ago by
Kasper Daniel Hansen
★ 6.5k
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Robert
▴ 10
0
votes
2
replies
1.6k
views
Rsamtools: scan all optional tags that exists in my bam file
Rsamtools
Rsamtools
updated 2.2 years ago by
Marcel Ramos
690 • written 10.6 years ago by
Guest User
★ 13k
0
votes
1
reply
1.5k
views
Rsamtools installation error
Rsamtools
Rsamtools
updated 10.4 years ago by
Dan Tenenbaum
★ 8.2k • written 10.4 years ago by
nishant thakur
▴ 10
0
votes
5
replies
1.9k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO
BSgenome
BSgenome
Rsamtools
genomes
MEDIPS
GO
BSgenome
BSgenome
Rsamtools
genomes
updated 10.1 years ago by
Martin Morgan
25k • written 10.1 years ago by
Vining, Kelly
▴ 220
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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