Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Alignment
•
reset
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
16
replies
1.9k
views
readGAlignmentPairs error
Alignment
Alignment
updated 10.6 years ago by
Hervé Pagès
16k • written 10.6 years ago by
Leonard Goldstein
▴ 80
0
votes
16
replies
2.5k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
7.6 years ago
Isaac Virshup
• 0
0
votes
16
replies
4.4k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.5 years ago
writetoroopali
• 0
5
votes
12
replies
7.7k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq
Alignment
edgeR
sva
updated 9.3 years ago by
Gordon Smyth
50k • written 10.0 years ago by
shirley zhang
★ 1.0k
0
votes
11
replies
5.7k
views
Biostring: print sequence alignment to file
Alignment
Biostrings
Alignment
Biostrings
updated 12.0 years ago by
Thomas Girke
★ 1.7k • written 12.1 years ago by
Martin Preusse
▴ 100
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa
alignment
visualization
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
tim.ivanov.92
• 0
0
votes
9
replies
2.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
5.4 years ago
A
▴ 40
0
votes
9
replies
1.9k
views
Mapping microarray probes to the genome using findOverlaps
Microarray
Alignment
Annotation
zebrafish
probe
Biostrings
GenomicFeatures
Microarray
updated 13.2 years ago by
Sean Davis
21k • written 13.2 years ago by
Hervé Pagès
16k
0
votes
8
replies
1.5k
views
memory exhausted for readAligned
Alignment
Alignment
updated 15.2 years ago by
Martin Morgan
25k • written 15.2 years ago by
Lana Schaffer
★ 1.3k
5
votes
8
replies
6.0k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam
sam
alignment
biostrings
9.2 years ago
ben.ward
▴ 30
0
votes
8
replies
3.1k
views
Annotation files for bacterial genome RNAseq
Alignment
Annotation
ASSIGN
Alignment
Annotation
ASSIGN
updated 9.9 years ago by
James W. MacDonald
65k • written 9.9 years ago by
José Luis Lavín
▴ 80
0
votes
8
replies
2.0k
views
Rsubread alingner
Alignment
Yeast
Rsubread
Alignment
Yeast
Rsubread
13.0 years ago
Wei Shi
★ 3.6k
0
votes
7
replies
1.6k
views
MEDIPS error extending reads
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 11.1 years ago by
Lukas Chavez
▴ 570 • written 11.1 years ago by
Stephen Turner
▴ 290
0
votes
7
replies
1.9k
views
about reduce function in GenomicRanges
Alignment
Alignment
12.3 years ago
Tarca, Adi
▴ 570
0
votes
7
replies
2.1k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment
Rattus norvegicus
BSgenome
BSgenome
QuasR
Alignment
Rattus norvegicus
BSgenome
updated 10.2 years ago by
Hervé Pagès
16k • written 10.2 years ago by
Guido Hooiveld
★ 3.9k
0
votes
7
replies
2.4k
views
obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment
probe
Alignment
probe
updated 11.8 years ago by
James W. MacDonald
65k • written 11.8 years ago by
shirley zhang
★ 1.0k
0
votes
6
replies
3.2k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster
quasR
genomicfeatures
genomicranges
alignment
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
Fiona
▴ 70
0
votes
6
replies
1.8k
views
Reading paired-end data into GRangesList
Alignment
Alignment
updated 12.5 years ago by
Paul Leo
▴ 970 • written 12.5 years ago by
Hubert Rehrauer
▴ 100
0
votes
6
replies
1.9k
views
Biostring: print sequence alignment to file
Alignment
Cancer
Biostrings
Alignment
Cancer
Biostrings
updated 11.8 years ago by
Martin Preusse
▴ 100 • written 11.8 years ago by
Hervé Pagès
16k
0
votes
6
replies
1.7k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment
BSgenome
safe
BSgenome
MEDIPS
Alignment
BSgenome
safe
BSgenome
MEDIPS
updated 10.4 years ago by
Lukas Chavez
▴ 570 • written 10.4 years ago by
Vining, Kelly
▴ 220
0
votes
5
replies
2.0k
views
filterBam
Alignment
Alignment
updated 10.8 years ago by
raffaele calogero
▴ 500 • written 10.8 years ago by
rcaloger
▴ 500
0
votes
5
replies
1.6k
views
Visualization of alignments with mismatch bases
SNP
Coverage
Alignment
Visualization
ggbio
SNP
Coverage
Alignment
Visualization
ggbio
updated 11.2 years ago by
Tengfei Yin
▴ 420 • written 11.2 years ago by
Michael Lawrence
★ 11k
1
vote
5
replies
4.7k
views
DiffBind error
Alignment
DiffBind
Alignment
DiffBind
updated 11.3 years ago by
Rory Stark
★ 5.2k • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
5
replies
1.4k
views
DECIPHER maximum allowable size
DECIPHER
Alignment
alig
updated 3.0 years ago by
Erik Wright
▴ 150 • written 3.0 years ago by
curiousmind007
▴ 10
0
votes
5
replies
1.8k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq
quasr
alignment
updated 8.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.4 years ago by
nadia_boufaied
• 0
0
votes
5
replies
1.5k
views
easyRNASeq - error reading single chromosome bam
RNASeq
Alignment
BSgenome
BSgenome
RNASeq
Alignment
BSgenome
BSgenome
updated 12.2 years ago by
delhomme@embl.de
★ 1.2k • written 12.2 years ago by
Lescai, Francesco
▴ 380
2
votes
5
replies
1.3k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment
GO
Cancer
BSgenome
BSgenome
Alignment
GO
Cancer
BSgenome
BSgenome
updated 10.9 years ago by
Martin Morgan
25k • written 10.9 years ago by
Guest User
★ 13k
0
votes
5
replies
1.7k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment
Cancer
convert
GenomicAlignments
Alignment
Cancer
convert
GenomicAlignments
updated 10.1 years ago by
Hervé Pagès
16k • written 10.1 years ago by
Niu, Liang NIH/NIEHS [E]
▴ 50
0
votes
5
replies
1.4k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment
Annotation
hgu133plus2
Alignment
Annotation
hgu133plus2
updated 15.5 years ago by
Hervé Pagès
16k • written 15.5 years ago by
Bazeley, Peter
▴ 10
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 10.1 years ago by
Lukas Chavez
▴ 570 • written 10.1 years ago by
Vining, Kelly
▴ 220
0
votes
5
replies
1.1k
views
GappedAlignmentPairs requests
Alignment
Cancer
GenomicRanges
Alignment
Cancer
GenomicRanges
updated 11.8 years ago by
Michael Lawrence
★ 11k • written 11.8 years ago by
Hervé Pagès
16k
0
votes
5
replies
1.9k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment
Biostrings
Alignment
Biostrings
13.8 years ago
Coghlan, Avril
▴ 190
0
votes
4
replies
1.5k
views
Howto annotate blast subject.id with AnnotationDbi
Alignment
GO
annotate
AnnotationDbi
Alignment
GO
annotate
AnnotationDbi
updated 10.9 years ago by
Marc Carlson
★ 7.2k • written 10.9 years ago by
Arnaud Mounier
▴ 40
0
votes
4
replies
1.7k
views
segfault for pairwiseAlignment
sequencing
software error
alignment
updated 9.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.6 years ago by
Taub, Margaret
▴ 10
0
votes
4
replies
1.7k
views
easyRNASeq error
Sequencing
Alignment
Annotation
Organism
BSgenome
biomaRt
BSgenome
easyRNASeq
Sequencing
12.2 years ago
delhomme@embl.de
★ 1.2k
2
votes
4
replies
2.1k
views
running msa (msa) aborts R session
msa
alignment
r
software error
written 6.4 years ago by
ans74
• 0
2
votes
4
replies
6.9k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing
Alignment
DESeq
DESeq2
Sequencing
Alignment
DESeq
DESeq2
updated 8.9 years ago by
gaelgarcia
• 0 • written 9.9 years ago by
Guest User
★ 13k
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings
iranges
sequence
alignment
protein
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
1.4k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 6.4 years ago by
Hervé Pagès
16k • written 6.4 years ago by
dhwani2410
• 0
0
votes
4
replies
1.7k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR
rnaseq
alignment
splicemap
bowtie2
8.1 years ago
Gabriella
• 0
3
votes
4
replies
1.5k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
thomas.dobrenel
• 0
0
votes
4
replies
1.7k
views
WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)
Alignment
Alignment
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
bach le
▴ 40
0
votes
4
replies
1.8k
views
nearly exact overlaps between GAlignmentPairs and GenomicRanges
Alignment
Alignment
9.7 years ago
Georg Otto
▴ 120
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
0
votes
3
replies
2.9k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment
BSgenome
PROcess
BSgenome
IRanges
MEDIPS
Alignment
BSgenome
PROcess
BSgenome
updated 10.7 years ago by
Lukas Chavez
▴ 570 • written 10.7 years ago by
Jonathan Ellis
▴ 40
3
votes
3
replies
1.6k
views
Reading large DNA alignments and keeping polymorphic sites
sequence
alignment
biostrings
updated 9.4 years ago by
Hervé Pagès
16k • written 9.4 years ago by
ben.ward
▴ 30
1
vote
3
replies
1.7k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment
Annotation
Organism
Schizosaccharomyces pombe
biomaRt
AnnotationForge
Alignment
updated 10.7 years ago by
Marc Carlson
★ 7.2k • written 10.7 years ago by
Marco Blanchette
▴ 220
0
votes
3
replies
1.4k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing
Alignment
GO
edgeR
DESeq2
updated 9.7 years ago by
Ryan C. Thompson
★ 7.9k • written 9.7 years ago by
Nick N
▴ 60
0
votes
3
replies
1.4k
views
homopolymer gap extension penalty in Biostrings
Sequencing
Alignment
GO
Cancer
Sequencing
Alignment
GO
Cancer
updated 12.2 years ago by
Noah Hoffman
▴ 10 • written 12.2 years ago by
Hervé Pagès
16k
50 results • Page
1 of 1
Recent ...
Replies
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
Awards
• All
Scholar
to
Rory Stark
★ 5.2k
Popular Question
to
tangming2005
▴ 190
Popular Question
to
Ian D.
▴ 70
Popular Question
to
junhui.li11
• 0
Scholar
to
James W. MacDonald
65k
Locations
• All
WEHI, Melbourne, Australia,
just now
United States,
2 minutes ago
Seattle, WA, United States,
4 minutes ago
United States,
39 minutes ago
United States,
46 minutes ago
Traffic: 553 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