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RSamtools
•
reset
1
vote
6
replies
3.0k
views
different results between Rsamtools::pileup and samtools depth
rsamtools
pileup
9.4 years ago
TimothéeFlutre
▴ 80
2
votes
1
reply
5.1k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam
rsamtools
samtools
genomicalignments
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
Vang Le
▴ 80
0
votes
1
reply
1.5k
views
Error with Rsamtools
Rsamtools
updated 9.5 years ago by
Martin Morgan
25k • written 9.5 years ago by
alex.tamburino
• 0
1
vote
7
replies
2.5k
views
Error installing cummeRbund/Rsamtools
cummerbund
rsamtools
package installation
compilation error
9.6 years ago • updated 9.5 years ago
rainer.rutka
▴ 10
1
vote
2
replies
1.5k
views
How to specify the illumina phred scoring scheme in RSamtools pileup function?
rsamtools
phred-scaled genotype quality
9.6 years ago
Pandurang Kolekar
▴ 10
0
votes
1
reply
1.1k
views
Rsamtools error Installation
rsamtools
9.6 years ago
mohit
• 0
0
votes
3
replies
1.8k
views
Rsamtools PileupParam set minimum depth to zero
rsamtools
pileup
9.7 years ago
komal.rathi
▴ 120
6
votes
3
replies
5.0k
views
Filtering a BAM file using RSamtools
rsamtools
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
Vivek.b
▴ 100
2
votes
4
replies
3.5k
views
getSeq{BSgenome} error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome
rsamtools
9.8 years ago
komal.rathi
▴ 120
0
votes
0
replies
885
views
Rsamtools scanTabix segfault
rsamtools
software error
9.8 years ago
heinig
• 0
1
vote
2
replies
2.1k
views
scanBam with ScanBamParam argument which specified ignores yieldSize. Intentionally?
scanbam
scanbamparam
rsamtools
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
Johannes Rainer
★ 2.1k
1
vote
2
replies
1.7k
views
Rsamtools pileup does not return reference base information
r
rsamtools
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
komal.rathi
▴ 120
1
vote
1
reply
1.2k
views
inconsistent default of file suffix
variantannotation
rsamtools
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
TimothéeFlutre
▴ 80
1
vote
13
replies
3.3k
views
Rsamtools memory leak
rsamtools
scanbam
bam
granges
iranges
10.0 years ago
mhills
▴ 10
0
votes
4
replies
1.4k
views
Is there support for tag type 'B' in Rsamtools?
rsamtools
software error
10.0 years ago
obanerjee
• 0
1
vote
1
reply
1.2k
views
Large BAM File
rsamtools
updated 10.0 years ago by
Hervé Pagès
16k • written 10.0 years ago by
yogi
• 0
5
votes
5
replies
4.8k
views
Error when reading bam file with duplicated header
rsamtools
genomicalignments
updated 10.0 years ago by
Michael Dondrup
▴ 10 • written 10.4 years ago by
Rene
▴ 20
0
votes
2
replies
1.5k
views
New to R: How to use your own data for Bioconductor Packages
MEDIPS
rsamtools
updated 10.1 years ago by
Dan Tenenbaum
★ 8.2k • written 10.1 years ago by
hseepany
• 0
1
vote
4
replies
2.3k
views
how to install Rsamtools in bioconductor/devel_base docker
docker
Rsamtools
10.2 years ago
Ou, Jianhong
★ 1.3k
2
votes
2
replies
3.0k
views
How to randomly sample BAM files
rsamtools
genomicalignments
genomicfiles
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
Welliton de Souza
▴ 70
0
votes
13
replies
3.0k
views
readGAlignments + BamViews not working in BioC-Devel
genomicalignments
rsamtools
10.2 years ago
Arne Muller
▴ 20
1
vote
2
replies
1.7k
views
Rsamtools and dbnsfp
bioconductor
rsamtools
annotation
variantannotation
10.2 years ago
jhomsy
• 0
5
votes
9
replies
2.9k
views
Reading alignments above a mapq threshold from BAM files
rsamtools
bam
updated 10.3 years ago by
Martin Morgan
25k • written 10.3 years ago by
Johannes Rainer
★ 2.1k
4
votes
4
replies
3.0k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup
rsamtools
bam
genomicalignments
updated 10.3 years ago by
Nathaniel Hayden
▴ 180 • written 10.3 years ago by
Sam Buckberry
• 0
0
votes
0
replies
968
views
seqbias : Suitable sampling
seqbias
rsamtools
10.4 years ago
Kaj Chokeshaiusaha
▴ 70
3
votes
12
replies
3.2k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools
cn.mops
installation
10.5 years ago
Spollen, William G.
▴ 30
0
votes
4
replies
1.5k
views
Rsamtools failing to parse PEDIGREE header
Rsamtools
updated 10.5 years ago by
Valerie Obenchain
★ 6.8k • written 10.5 years ago by
Jonathan Ellis
• 0
2
votes
4
replies
2.5k
views
Editing of GAlignments
granges
rsamtools
bioconductor
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
gen
▴ 30
1
vote
1
reply
1.5k
views
removing reads from coverage() calculation.
bam
rsamtools
genomicranges
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
gen
▴ 30
0
votes
1
reply
1.3k
views
summarizeOverlaps on partial BAM file?
GenomicFeatures
GRange
Rsamtools
updated 10.7 years ago by
Valerie Obenchain
★ 6.8k • written 10.7 years ago by
cidster12
• 0
4
votes
5
replies
2.7k
views
scanBam on BamSampler supposed to be fast?
rsamtools
bam
updated 10.7 years ago by
Martin Morgan
25k • written 10.7 years ago by
Johannes Rainer
★ 2.1k
1
vote
2
replies
2.8k
views
Processing bam files by read group
rsamtools
read group
bam
updated 10.8 years ago by
Nathaniel Hayden
▴ 180 • written 10.9 years ago by
Thomas Sandmann
▴ 90
1
vote
3
replies
1.4k
views
Rsamtools error with long read sets
rsamtools
software error
updated 11.0 years ago by
Martin Morgan
25k • written 11.0 years ago by
wtimp0
▴ 10
0
votes
2
replies
1.2k
views
Error handling with Rsamtools
rsamtools
updated 11.0 years ago by
Martin Morgan
25k • written 11.0 years ago by
t.kuilman
▴ 170
0
votes
0
replies
1.5k
views
[devteam-bioc] parallel BAM sorting with Rsamtools
Cancer
Rsamtools
BiocParallel
11.1 years ago
Jens Reeder
▴ 40
0
votes
1
reply
1.6k
views
Thread safety of BSgenome getSeq()
Cancer
BSgenome
PROcess
BSgenome
Rsamtools
Cancer
BSgenome
PROcess
BSgenome
Rsamtools
updated 11.3 years ago by
Hervé Pagès
16k • written 11.3 years ago by
Jeff Johnston
▴ 90
0
votes
4
replies
1.9k
views
GenomicAlignments and QNAME collision
RNASeq
Cancer
convert
Rsamtools
GenomicAlignments
RNASeq
Cancer
convert
Rsamtools
updated 11.3 years ago by
Stefano Calza
▴ 90 • written 11.4 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
2.4k
views
It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment
GO
Cancer
BSgenome
BSgenome
Rsamtools
genomes
MEDIPS
Alignment
GO
Cancer
updated 11.5 years ago by
Lukas Chavez
▴ 570 • written 11.5 years ago by
Vining, Kelly
▴ 220
0
votes
1
reply
2.1k
views
So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment
GO
Cancer
BSgenome
BSgenome
Rsamtools
genomes
MEDIPS
Alignment
GO
Cancer
updated 11.5 years ago by
Lukas Chavez
▴ 570 • written 11.5 years ago by
Vining, Kelly
▴ 220
0
votes
5
replies
2.4k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO
BSgenome
BSgenome
Rsamtools
genomes
MEDIPS
GO
BSgenome
BSgenome
Rsamtools
genomes
updated 11.5 years ago by
Martin Morgan
25k • written 11.5 years ago by
Vining, Kelly
▴ 220
0
votes
2
replies
1.5k
views
MEDIPS.createSet error
BSgenome
BSgenome
Rsamtools
MEDIPS
BSgenome
BSgenome
Rsamtools
MEDIPS
updated 11.5 years ago by
Lukas Chavez
▴ 570 • written 11.5 years ago by
Vining, Kelly
▴ 220
0
votes
9
replies
3.3k
views
Problems Counting Reads with summarizeOverlaps
biomaRt
Rsamtools
biomaRt
Rsamtools
updated 11.8 years ago by
Valerie Obenchain
★ 6.8k • written 11.8 years ago by
Sam McInturf
▴ 300
0
votes
1
reply
1.9k
views
Rsamtools installation error
Rsamtools
Rsamtools
updated 11.8 years ago by
Dan Tenenbaum
★ 8.2k • written 11.8 years ago by
nishant thakur
▴ 10
0
votes
2
replies
2.1k
views
Rsamtools: scan all optional tags that exists in my bam file
Rsamtools
Rsamtools
updated 3.6 years ago by
Marcel Ramos
700 • written 12.0 years ago by
Guest User
★ 13k
0
votes
1
reply
987
views
[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage
Cancer
Rsamtools
Coverage
Cancer
Rsamtools
12.1 years ago
Hervé Pagès
16k
0
votes
2
replies
3.5k
views
Rsamtools: sortBam() and 'samtools sort' does not give the same results
Alignment
Rsamtools
Alignment
Rsamtools
updated 12.1 years ago by
Martin Morgan
25k • written 12.1 years ago by
Henrik Bengtsson
★ 2.4k
0
votes
4
replies
1.7k
views
IRanges::unlist in package
rtracklayer
IRanges
GenomicFeatures
Rsamtools
rtracklayer
IRanges
GenomicFeatures
Rsamtools
updated 12.2 years ago by
James W. MacDonald
68k • written 12.2 years ago by
Marco Blanchette
▴ 220
0
votes
1
reply
2.1k
views
Access source code of internal function within R
Rsamtools
Rsamtools
updated 12.2 years ago by
Dan Tenenbaum
★ 8.2k • written 12.2 years ago by
heyi xiao
▴ 360
0
votes
7
replies
3.7k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation
PROcess
Rsamtools
VariantAnnotation
VariantAnnotation
PROcess
Rsamtools
updated 12.4 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.4 years ago by
UBod
▴ 300
0
votes
1
reply
1.4k
views
summarizeOverlaps mode ignoring inter feature overlaps
GenomicRanges
Rsamtools
GenomicRanges
Rsamtools
updated 12.4 years ago by
Thomas Girke
★ 1.7k • written 12.4 years ago by
Valerie Obenchain
★ 6.8k
186 results • Page
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