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RSAMTOOLS
•
reset
0
votes
2
replies
445
views
Installation error for Rsamtools.
Rsamtools
updated 8 months ago by
ATpoint
★ 4.9k • written 8 months ago by
Sheila
• 0
2
votes
1
reply
661
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
maltethodberg
▴ 180
0
votes
0
replies
923
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
23 months ago
Xinqi
• 0
0
votes
0
replies
673
views
[Rsamtools] pileup option max_depth behaviour
Rsamtools
pileup
2.2 years ago
romain.lannes
• 0
0
votes
0
replies
805
views
How to speed up pileup from Rsamtools?
Rsamtools
pileup
2.4 years ago
alexandr.gopanenko
▴ 50
2
votes
4
replies
3.2k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Christopher
• 0
0
votes
0
replies
787
views
Rsamtools pileup help
Rsamtools
pileup
2.7 years ago
JoeMG
• 0
0
votes
1
reply
1.1k
views
Samtools markdup in Rsamtools
Rsamtools
updated 2.7 years ago by
Martin Morgan
25k • written 2.7 years ago by
Learner
• 0
0
votes
2
replies
1.4k
views
scanBam
Rsamtools
Rsam
updated 2.7 years ago by
Martin Morgan
25k • written 2.7 years ago by
jojo.valensi
• 0
1
vote
0
replies
838
views
Data format format for summarising each NGS read without collapsing into a count
DataRepresentation
exSTRa
Rsamtools
3.1 years ago
Rick
▴ 10
3
votes
2
replies
1.6k
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
3.2 years ago • updated 3.1 years ago
Jiping Wang
▴ 90
4
votes
13
replies
5.5k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
etiennedanis
• 0
0
votes
0
replies
1.2k
views
failed to open file using Signac maybe related to Rsamstools
Rsamtools
3.5 years ago
Haemin
• 0
1
vote
0
replies
1.5k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
3.5 years ago
L
▴ 50
0
votes
18
replies
5.5k
views
Indexing FASTA file using RSamtools
Rsamtools
GenomicFeatures
3.7 years ago • updated 3.6 years ago
rbenel
▴ 50
0
votes
0
replies
928
views
confused interpreting results from scanBam in RSamtools
Rsamtools
Rsa
3.7 years ago
sara
• 0
0
votes
0
replies
1.0k
views
Rsamtools and data.table OR advice of packages
data.table
Rsamtools
NGS
3.7 years ago
sara
• 0
1
vote
3
replies
2.6k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped
RNAseq
Rsamtools
3.9 years ago
polemiraza
▴ 70
0
votes
0
replies
946
views
Difficulty exporting consensus sequence from bam file
Rsamtools
sequenceLayer
4.3 years ago
mike_flower
• 0
0
votes
1
reply
1.1k
views
Rsamtools: how to output base positions on reads
Rsamtools
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
yuharasatoshi
• 0
4
votes
9
replies
2.5k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools
Biostrings
updated 4.3 years ago by
Hervé Pagès
16k • written 4.4 years ago by
Jon Bråte
▴ 270
1
vote
1
reply
1.3k
views
could not find function "scanBam"
Rsamtool
Rsamtools
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
jbzhang2012
• 0
0
votes
1
reply
1.0k
views
Issue with Rsamtools reading a remote file on Windows
Rsamtools
updated 4.1 years ago by
Divya
• 0 • written 4.4 years ago by
cthangav
• 0
2
votes
1
reply
1.2k
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 4.5 years ago by
Mike Smith
★ 6.6k • written 4.5 years ago by
Jeremy
▴ 10
2
votes
2
replies
1.5k
views
RSamtools idxstats does not return unmapped reads
Rsamtools
4.5 years ago
mja18
▴ 40
1
vote
2
replies
1.6k
views
RSamtools idxstatsBam not working with remote bam file
Rsamtools
4.5 years ago
mja18
▴ 40
2
votes
4
replies
3.5k
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
4.5 years ago
sbcn
▴ 80
3
votes
5
replies
3.7k
views
Split a BAM file with read groups
readgroup
bam
Rsamtools
4.5 years ago
sbcn
▴ 80
0
votes
2
replies
1.3k
views
Visualising read alignments in
GenomicAlignments
Rsamtools
written 4.6 years ago by
Joshua
• 0
4
votes
4
replies
5.3k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 4.6 years ago by
changxu.fan
▴ 20
2
votes
6
replies
1.8k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
4.6 years ago
robmaz77
▴ 20
0
votes
2
replies
1.8k
views
Support for CSI indexes in Rsamtools
Rsamtools
4.9 years ago • updated 4.8 years ago
bernatgel
▴ 150
6
votes
5
replies
4.4k
views
Extracting Sequences from Fasta Files with Rsamtools
Rsamtools
updated 4.9 years ago by
Martin Morgan
25k • written 5.3 years ago by
jlee
▴ 20
0
votes
0
replies
1.1k
views
How to get sequence size of insertion/deletion in sam file pileup (e.g. using Rsamtools)
Rsamtools
pileup
insertion
deletion
5.1 years ago
madsheilskov
▴ 10
12
votes
5
replies
5.4k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 14 months ago by
Paul
• 0 • written 5.3 years ago by
yusuke_suita
▴ 40
2
votes
2
replies
1.8k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 5.4 years ago by
Hervé Pagès
16k • written 5.4 years ago by
Robert
▴ 10
0
votes
5
replies
2.1k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
rita.monteiro
• 0
0
votes
1
reply
957
views
RSAMTOOLS to analyse BED FILES
RSAMTOOLS
BED-FILE
5.4 years ago
r.mulder01
• 0
4
votes
3
replies
1.5k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools
summarizeOverlaps
RNA-seq
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
liorglic
▴ 10
1
vote
2
replies
1.3k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools
GenomicAlignments
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
Graeme Thorn
▴ 10
0
votes
1
reply
984
views
Subsetting the bamfile by readlength and extracting the information about distribution the SNV across these reads length
Rsamtools
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
alexandr.gopanenko
▴ 50
1
vote
6
replies
3.2k
views
Rsamtools pileup function
Rsamtools
pileup
number of reads
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
mgray
▴ 10
0
votes
2
replies
1.5k
views
Problem with scanBam functiuon in Rsamools
Rsamtools
scanBAM
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
owen.donohoe
• 0
0
votes
0
replies
1.5k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
5.9 years ago
ATpoint
★ 4.9k
5
votes
15
replies
2.5k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 6.0 years ago by
Hervé Pagès
16k • written 6.1 years ago by
Gordon Smyth
53k
0
votes
1
reply
1.7k
views
Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
Rsamtools
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
Jiping Wang
▴ 90
0
votes
1
reply
1.3k
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi
bumphunter
Rsamtools
6.2 years ago
Boran Gao
• 0
1
vote
8
replies
3.8k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools
GenomicAlignments
RNA-seq coverage score
updated 6.3 years ago by
Hervé Pagès
16k • written 6.3 years ago by
Jiping Wang
▴ 90
1
vote
1
reply
1.5k
views
Excluding reads with a certain tag using tagFilter from Rsamtools
rsamtools
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
liz.ingsimmons
▴ 140
9
votes
32
replies
9.1k
views
Rsamtools v 1.99.6 installation error
Rsamtools
BiocManager
R 3.6
ubuntu
updated 6.4 years ago by
Hervé Pagès
16k • written 6.4 years ago by
kubovcij
• 0
186 results • Page
1 of 4
Recent ...
Replies
Answer: Gatins Set error
by
James W. MacDonald
68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins?
by
Gordon Smyth
53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function
by
Gordon Smyth
53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub
by
Aaron Lun
★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package
by
ATpoint
★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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