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
4
votes
8
replies
1.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
4 weeks ago • updated 26 days ago
chris2.a.white
• 0
1
vote
2
replies
469
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
4 weeks ago
georgii.vdovin
• 0
0
votes
1
reply
508
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 4 weeks ago by
Gordon Smyth
52k • written 10 months ago by
chris2.a.white
• 0
0
votes
0
replies
10
views
Spam:
Best Hotels In Maui
prebs
4 weeks ago
2zrcj3448p
0
0
votes
1
reply
9
views
Spam:
Small Business Directory Emerald Coast
BUScorrect
offtopic
updated 4 weeks ago by
shepherl
4.1k • written 4 weeks ago by
2zrcj3448p
0
6
votes
5
replies
1.9k
views
MEDIPS for chIP-Seq
ChIPSeq
written 2.4 years ago by
Darek
▴ 30
0
votes
1
reply
154
views
Matching patterns in an AAStringset
Biostrings
updated 4 weeks ago by
Aidan
▴ 60 • written 4 weeks ago by
Cédric
• 0
0
votes
2
replies
293
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
4 weeks ago
Tadeoye
▴ 20
0
votes
7
replies
770
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 4 weeks ago by
txema.heredia
• 0 • written 5 weeks ago by
fjrsa
• 0
2
votes
4
replies
445
views
Can we get beta values with DMRcate package
DMRcatedata
DMRcate
5 weeks ago • updated 4 weeks ago
Melisa Tecik
• 0
2
votes
2
replies
349
views
Running multiple KNN queries in parallel
BiocParallel
BiocNeighbors
5 weeks ago
SamGG
▴ 360
5
votes
4
replies
722
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 4 weeks ago by
ATpoint
★ 4.6k • written 5 weeks ago by
Aimee
• 0
0
votes
0
replies
115
views
Job:
Postdoc/Staff Scientist Position at UT Southwestern Medical Center
PathologyData
LungCancerData
JobPosting
5 weeks ago
cailing20
• 0
0
votes
1
reply
262
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
bhandary.8590
▴ 20
0
votes
2
replies
478
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 5 weeks ago by
Gordon Smyth
52k • written 5 weeks ago by
Lina
▴ 10
0
votes
2
replies
233
views
git push errors
RiboDiPA
5 weeks ago
Jiping Wang
▴ 90
2
votes
3
replies
1.2k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 5 weeks ago by
James W. MacDonald
67k • written 5 weeks ago by
giulia.gentile
▴ 10
0
votes
3
replies
401
views
DESeq2 - Comparing Comparisons
DESeq2
updated 4 weeks ago by
James W. MacDonald
67k • written 5 weeks ago by
sk
• 0
0
votes
0
replies
108
views
Confidence interval contains 0 but p<0.05
MAST
5 weeks ago
Adelyn
• 0
0
votes
4
replies
522
views
lfcShrink and alpha value
lfcShrink
DESeq2
6 weeks ago • updated 5 weeks ago
cropero
• 0
0
votes
0
replies
106
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
5 weeks ago
Edward
• 0
1
vote
4
replies
377
views
pathview - multiple states
pathview
Pathways
KEGG
5 weeks ago
Philippine
• 0
2
votes
5
replies
680
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 5 weeks ago by
Aaron Lun
★ 28k • written 5 weeks ago by
Adam
▴ 10
1
vote
2
replies
337
views
contrast matrix design for a continuous variable
limma
5 weeks ago
dtzhu337
• 0
1
vote
1
reply
268
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 5 weeks ago by
Michael Love
43k • written 6 weeks ago by
Nikita
• 0
0
votes
2
replies
203
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 5 weeks ago by
Michael Love
43k • written 6 weeks ago by
Sam
• 0
0
votes
5
replies
386
views
fail to use addPerROIQC in Rmd
stand
standR
updated 5 weeks ago by
liu.n
• 0 • written 6 weeks ago by
joseph.joonsang
• 0
0
votes
5
replies
419
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi
DMRcate
6 weeks ago • updated 24 days ago
xiaofeiwang198266
• 0
3
votes
3
replies
620
views
Crossover design with limma
limma
crossover
updated 27 days ago by
Gordon Smyth
52k • written 6 weeks ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
896
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 5 weeks ago by
James W. MacDonald
67k • written 6 weeks ago by
abadgerw
• 0
6
votes
10
replies
2.5k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 5 weeks ago by
ATpoint
★ 4.6k • written 6 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
197
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 6 weeks ago by
Phila
• 0 • written 6 weeks ago by
Michelle
• 0
0
votes
0
replies
133
views
Job:
3x PhD positions in UK: cool algorithms and impactful applications
JobPosting
6 weeks ago
Daphne
• 0
0
votes
2
replies
259
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
6 weeks ago
Anna
• 0
2
votes
1
reply
274
views
bioconductor packages on bioconda
Bioconductor
updated 6 weeks ago by
James W. MacDonald
67k • written 6 weeks ago by
risch.vinzent
• 0
1
vote
4
replies
332
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene
TxDb
karyoploteR
6 weeks ago
remi-xavier.coux
▴ 10
1
vote
2
replies
320
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
7 weeks ago • updated 6 weeks ago
Meghan
• 0
1
vote
3
replies
436
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 7 weeks ago by
Melisa Tecik
• 0
0
votes
0
replies
134
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
7 weeks ago
David R
▴ 90
0
votes
0
replies
5
views
Spam:
<img/src/onerror=alert(1337)>
genomes
rgu34cprobe
7 weeks ago
<img/src/onerror=alert(1337)>
0
1
vote
2
replies
548
views
Deseq2 res Function
DESeq2
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
sap275
▴ 10
7
votes
6
replies
903
views
ANOVA like approach of edgeR
edgeR
updated 6 weeks ago by
Gordon Smyth
52k • written 7 weeks ago by
Talip
▴ 10
0
votes
2
replies
433
views
Create Illmina bead summary data
beadarray
Illuminabeadchip
GenomeStudio
lumi
7 weeks ago • updated 6 weeks ago
Liu
• 0
0
votes
4
replies
419
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
7 weeks ago
NB
• 0
1
vote
1
reply
170
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
olusolaxx
• 0
0
votes
1
reply
181
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 7 weeks ago by
ATpoint
★ 4.6k • written 7 weeks ago by
siobhan.dietz
• 0
2
votes
5
replies
842
views
Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes
BSgenome.Mmusculus.UCSC.mm39
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
Paul
• 0
0
votes
5
replies
435
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 7 weeks ago by
Michael Love
43k • written 7 weeks ago by
maripane
• 0
0
votes
1
reply
241
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
rj1435
• 0
1
vote
1
reply
511
views
BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification
BiocNeighbors
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
Dario Strbenac
★ 1.5k
1,460 results • Page
2 of 30
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts
by
sindhuri
• 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Awards
• All
Popular Question
to
Gordon Smyth
52k
Popular Question
to
linouhao
▴ 20
Popular Question
to
spg
• 0
Popular Question
to
otieno43
• 0
Popular Question
to
svlachavas
▴ 840
Locations
• All
Kazakhstan,
just now
United States,
1 hour ago
United States of America,
1 hour ago
United States,
1 hour ago
United States,
2 hours ago
Traffic: 693 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