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rsamtools
•
reset
0
votes
2
replies
243
views
Installation error for Rsamtools.
Rsamtools
updated 11 weeks ago by
ATpoint
★ 4.8k • written 12 weeks ago by
Sheila
• 0
0
votes
1
reply
502
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
maltethodberg
▴ 180
0
votes
0
replies
759
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
17 months ago
Xinqi
• 0
0
votes
0
replies
572
views
[Rsamtools] pileup option max_depth behaviour
Rsamtools
pileup
20 months ago
romain.lannes
• 0
0
votes
0
replies
690
views
How to speed up pileup from Rsamtools?
Rsamtools
pileup
23 months ago
alexandr.gopanenko
▴ 50
2
votes
4
replies
2.7k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Christopher
• 0
0
votes
0
replies
701
views
Rsamtools pileup help
Rsamtools
pileup
2.2 years ago
JoeMG
• 0
0
votes
1
reply
981
views
Samtools markdup in Rsamtools
Rsamtools
updated 2.2 years ago by
Martin Morgan
25k • written 2.2 years ago by
Learner
• 0
0
votes
2
replies
1.3k
views
scanBam
Rsamtools
Rsam
updated 2.2 years ago by
Martin Morgan
25k • written 2.2 years ago by
jojo.valensi
• 0
1
vote
0
replies
721
views
Data format format for summarising each NGS read without collapsing into a count
DataRepresentation
exSTRa
Rsamtools
2.6 years ago
Rick
▴ 10
3
votes
2
replies
1.4k
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
2.6 years ago
Jiping Wang
▴ 90
4
votes
13
replies
5.0k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 2.8 years ago by
etiennedanis
• 0
0
votes
0
replies
1.1k
views
failed to open file using Signac maybe related to Rsamstools
Rsamtools
3.0 years ago
Haemin
• 0
1
vote
0
replies
1.3k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
3.0 years ago
L
▴ 50
0
votes
18
replies
4.9k
views
Indexing FASTA file using RSamtools
Rsamtools
GenomicFeatures
3.2 years ago • updated 3.1 years ago
rbenel
▴ 40
0
votes
0
replies
848
views
confused interpreting results from scanBam in RSamtools
Rsamtools
Rsa
3.2 years ago
sara
• 0
0
votes
0
replies
931
views
Rsamtools and data.table OR advice of packages
data.table
Rsamtools
NGS
3.2 years ago
sara
• 0
1
vote
3
replies
2.4k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped
RNAseq
Rsamtools
3.4 years ago
polemiraza
▴ 70
0
votes
0
replies
866
views
Difficulty exporting consensus sequence from bam file
Rsamtools
sequenceLayer
3.8 years ago
mike_flower
• 0
0
votes
1
reply
987
views
Rsamtools: how to output base positions on reads
Rsamtools
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
yuharasatoshi
• 0
4
votes
9
replies
2.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools
Biostrings
updated 3.8 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Jon Bråte
▴ 260
1
vote
1
reply
1.2k
views
could not find function "scanBam"
Rsamtool
Rsamtools
updated 3.9 years ago by
Martin Morgan
25k • written 3.9 years ago by
jbzhang2012
• 0
0
votes
1
reply
941
views
Issue with Rsamtools reading a remote file on Windows
Rsamtools
updated 3.6 years ago by
Divya
• 0 • written 3.9 years ago by
cthangav
• 0
2
votes
1
reply
1.1k
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 4.0 years ago by
Mike Smith
★ 6.6k • written 4.0 years ago by
Jeremy
▴ 10
2
votes
2
replies
1.3k
views
RSamtools idxstats does not return unmapped reads
Rsamtools
4.0 years ago
mja18
▴ 40
1
vote
2
replies
1.4k
views
RSamtools idxstatsBam not working with remote bam file
Rsamtools
4.0 years ago
mja18
▴ 40
2
votes
4
replies
3.1k
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
4.0 years ago
sbcn
▴ 80
3
votes
5
replies
3.4k
views
Split a BAM file with read groups
readgroup
bam
Rsamtools
4.0 years ago
sbcn
▴ 80
0
votes
2
replies
1.2k
views
Visualising read alignments in
GenomicAlignments
Rsamtools
written 4.1 years ago by
Joshua
• 0
4
votes
4
replies
4.9k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 4.1 years ago by
changxu.fan
▴ 20
2
votes
6
replies
1.6k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
4.1 years ago
robmaz77
▴ 20
0
votes
2
replies
1.6k
views
Support for CSI indexes in Rsamtools
Rsamtools
4.4 years ago • updated 4.3 years ago
bernatgel
▴ 150
6
votes
5
replies
4.2k
views
Extracting Sequences from Fasta Files with Rsamtools
Rsamtools
updated 4.4 years ago by
Martin Morgan
25k • written 4.8 years ago by
jlee
▴ 20
0
votes
0
replies
987
views
How to get sequence size of insertion/deletion in sam file pileup (e.g. using Rsamtools)
Rsamtools
pileup
insertion
deletion
4.6 years ago
madsheilskov
▴ 10
12
votes
5
replies
5.0k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 8 months ago by
Paul
• 0 • written 4.8 years ago by
yusuke_suita
▴ 40
2
votes
2
replies
1.6k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 4.9 years ago by
Hervé Pagès
16k • written 4.9 years ago by
Robert
▴ 10
0
votes
5
replies
1.9k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 4.9 years ago by
Kevin Blighe
★ 4.0k • written 4.9 years ago by
rita.monteiro
• 0
0
votes
1
reply
873
views
RSAMTOOLS to analyse BED FILES
RSAMTOOLS
BED-FILE
4.9 years ago
r.mulder01
• 0
4
votes
3
replies
1.4k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools
summarizeOverlaps
RNA-seq
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
liorglic
▴ 10
1
vote
2
replies
1.2k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools
GenomicAlignments
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
Graeme Thorn
▴ 10
0
votes
1
reply
870
views
Subsetting the bamfile by readlength and extracting the information about distribution the SNV across these reads length
Rsamtools
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
alexandr.gopanenko
▴ 50
1
vote
6
replies
2.9k
views
Rsamtools pileup function
Rsamtools
pileup
number of reads
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
mgray
▴ 10
0
votes
2
replies
1.3k
views
Problem with scanBam functiuon in Rsamools
Rsamtools
scanBAM
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
owen.donohoe
• 0
0
votes
0
replies
1.4k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
5.4 years ago
ATpoint
★ 4.8k
5
votes
15
replies
2.3k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 5.5 years ago by
Hervé Pagès
16k • written 5.6 years ago by
Gordon Smyth
52k
0
votes
1
reply
1.6k
views
Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
Rsamtools
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
Jiping Wang
▴ 90
0
votes
1
reply
1.2k
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi
bumphunter
Rsamtools
5.7 years ago
Boran Gao
• 0
1
vote
8
replies
3.5k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools
GenomicAlignments
RNA-seq coverage score
updated 5.8 years ago by
Hervé Pagès
16k • written 5.8 years ago by
Jiping Wang
▴ 90
1
vote
1
reply
1.3k
views
Excluding reads with a certain tag using tagFilter from Rsamtools
rsamtools
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
liz.ingsimmons
▴ 140
9
votes
32
replies
8.1k
views
Rsamtools v 1.99.6 installation error
Rsamtools
BiocManager
R 3.6
ubuntu
updated 5.9 years ago by
Hervé Pagès
16k • written 5.9 years ago by
kubovcij
• 0
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