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 :
summarizeOverlaps
•
reset
0
votes
0
replies
1.0k
views
Counting reads in genes with summarizeOverlaps
genomicAlignments
summarizeOverlaps
4.4 years ago
dequattro.concetta
▴ 10
4
votes
3
replies
1.2k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools
summarizeOverlaps
RNA-seq
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
liorglic
▴ 10
0
votes
9
replies
1.7k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps
R
GenomicAlignments
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
cavery
• 0
1
vote
9
replies
1.6k
views
Memory issues in summarizeOverlaps funtion
memory
summarizeOverlaps
updated 5.8 years ago by
James W. MacDonald
67k • written 5.8 years ago by
Diana
▴ 10
0
votes
1
reply
1.2k
views
counting reads with muliple hits with SummarizeOverlaps
R
seq
ngs
summarizeoverlaps
updated 6.6 years ago by
Valerie Obenchain
★ 6.8k • written 6.6 years ago by
Lolla
• 0
2
votes
2
replies
1.2k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps
genomicalignments
updated 6.6 years ago by
Valerie Obenchain
★ 6.8k • written 6.6 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
0
replies
1.1k
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
6.6 years ago
A
▴ 40
0
votes
0
replies
1.3k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments
rsamtools
BamViews
summarizeoverlaps
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
alex.gos90
▴ 10
1
vote
6
replies
1.8k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps
rangedsummarizedexperiment
grangeslist
summarizedexperiment
6.7 years ago
cosmin
• 0
0
votes
2
replies
1.2k
views
Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps
R
updated 6.7 years ago by
Valerie Obenchain
★ 6.8k • written 6.7 years ago by
Lolla
• 0
1
vote
1
reply
2.1k
views
How can I retrieve the gene names of my count matrix?
rnaseq
summarizeoverlaps
count matrix
updated 6.8 years ago by
James W. MacDonald
67k • written 6.8 years ago by
johnsonn573
• 0
1
vote
1
reply
2.3k
views
Difference between SummarizeOverlaps and HTSeq
R
summarizeoverlaps
htseqcounts
updated 7.0 years ago by
thokall
▴ 160 • written 7.0 years ago by
Walter F. Baumann
▴ 10
1
vote
2
replies
1.2k
views
Problems with summarizeOverlaps
bioconductor
rnaseq
summarizeoverlaps
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
Walter F. Baumann
▴ 10
1
vote
0
replies
1.3k
views
generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps
paired-end reads
readGAlignmentPairs
7.6 years ago
teresati
▴ 10
1
vote
1
reply
1.5k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps
rnaseq
updated 7.7 years ago by
Hervé Pagès
16k • written 7.7 years ago by
Walter F. Baumann
▴ 10
3
votes
3
replies
1.9k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps
R
bioconductor
rnaseq
rna-seq
updated 7.7 years ago by
Hervé Pagès
16k • written 7.7 years ago by
Walter F. Baumann
▴ 10
2
votes
2
replies
990
views
question about summrizeOverlaps
summarizeoverlaps
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
Ou, Jianhong
★ 1.3k
0
votes
1
reply
1.3k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments
summarizeoverlaps
updated 7.7 years ago by
James W. MacDonald
67k • written 7.7 years ago by
JunLVI
▴ 40
2
votes
6
replies
1.6k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite
bioconductor
summarizeoverlaps
genomicfeatures
genomicalignments
updated 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
BioinfStudent
• 0
2
votes
3
replies
2.3k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R
rnaseq
tophat
summarizeoverlaps
systempiper
updated 8.0 years ago by
Thomas Girke
★ 1.7k • written 8.0 years ago by
abass.conteh
• 0
1
vote
1
reply
2.3k
views
Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
software error
summarizeoverlaps
biocParallel
8.2 years ago
chriad
▴ 10
0
votes
5
replies
1.9k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps
genomicalignments
8.2 years ago
philipp.wahle
• 0
4
votes
3
replies
3.1k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps
rnaseq
bplapply
rangedsummarizedexperiment
read counting
8.4 years ago
ErickF
▴ 40
2
votes
2
replies
1.8k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 7 months ago by
isaac.vock
• 0 • written 8.4 years ago by
Jon Manning
▴ 90
2
votes
9
replies
1.9k
views
SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
jean.keller
▴ 10
0
votes
3
replies
1.9k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
8.7 years ago
vedran.franke
• 0
2
votes
7
replies
2.4k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps
bedtools
8.7 years ago
tmartinez
• 0
0
votes
1
reply
1.2k
views
No reads with summarizeOverlaps
summarizeoverlaps
rnaseq
8.7 years ago
diogo.camacho.2008
• 0
0
votes
2
replies
1.7k
views
Question about the function "summarizeOverlaps"
genomicalignments
summarizeoverlaps
updated 8.7 years ago by
Michael Love
42k • written 8.7 years ago by
myf3748
• 0
0
votes
1
reply
1.7k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps
bacteria
e coli
unique reads
updated 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
as9309
• 0
4
votes
11
replies
2.6k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps
summarizedexperiment
count matrix
low counts
rna-seq
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
shania90.lk
▴ 10
1
vote
4
replies
1.6k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
Tarca, Adi
▴ 570
2
votes
4
replies
2.7k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps
RNAseq
annotation
counts
8.8 years ago
bioprog
• 0
1
vote
2
replies
1.2k
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 8.9 years ago by
Steve Lianoglou
★ 13k • written 8.9 years ago by
glipori
• 0
2
votes
5
replies
3.1k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps
GAGE
updated 9.0 years ago by
Valerie Obenchain
★ 6.8k • written 9.0 years ago by
user31888
▴ 30
0
votes
3
replies
1.6k
views
Default Rapidr invalid class “SummarizedExperiment”
software error
RAPIDR
summarizeoverlaps
R
9.2 years ago • updated 9.1 years ago
Pau Marc Muñoz Torres
▴ 20
8
votes
9
replies
6.2k
views
could not find symbol "keepNA" in environment of the generic function
R
function
genomicalignments
genomicranges
summarizeoverlaps
updated 9.3 years ago by
Mathilde
• 0 • written 9.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
20
replies
6.8k
views
SummarizeOverlaps in R
summarizeoverlaps
Bam
rstudio
updated 9.3 years ago by
Jake
▴ 90 • written 9.3 years ago by
Lillyhchen
▴ 10
11
votes
8
replies
4.8k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps
genomicalignments
updated 9.6 years ago by
Hervé Pagès
16k • written 9.7 years ago by
rxzlmn
▴ 10
0
votes
1
reply
1.8k
views
tuning memory consumption of summarizeOverlaps?
rna-seq
summarizeoverlaps
updated 9.7 years ago by
Valerie Obenchain
★ 6.8k • written 9.7 years ago by
Vincent J. Carey, Jr.
6.7k
6
votes
14
replies
6.3k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments
RNASeq
genomicfeatures
summarizeoverlaps
updated 9.9 years ago by
Gordon Smyth
51k • written 9.9 years ago by
bioprog
• 0
0
votes
3
replies
2.6k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq
summarizeOverlaps
deseq2
tophat
genomicalignments
updated 10.0 years ago by
Dan Tenenbaum
★ 8.2k • written 10.0 years ago by
alejandro.colaneri
▴ 20
42 results • Page
1 of 1
Recent ...
Replies
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
dseauer
• 0
Thank you so much for all of your help! I really appreciate it!
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
Gordon Smyth
51k
Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
dseauer
• 0
Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…
Comment: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Stefano Mangiola
▴ 20
Thansk Herve', I will try. For reference this is the parallelization implementation of zellkonverter, to save anndata from SCE https://gi…
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
by
Jason
• 0
Any update on the resolution to this? I'm having the same issue with another species.
Votes
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
biomaRt rnorvegicus_gene_ensembl not available anymore
A: Does edgeR need to specify reference group?
Awards
• All
Commentator
to
James W. MacDonald
67k
Popular Question
to
Stefano Mangiola
▴ 20
Popular Question
to
Shian Su
▴ 40
Popular Question
to
altintas.ali
• 0
Popular Question
to
eve.olszanowski
• 0
Locations
• All
Australia,
1 minute ago
United States,
6 minutes ago
France,
12 minutes ago
China,
16 minutes ago
United Kingdom,
17 minutes ago
Traffic: 536 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