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
0
votes
2
replies
815
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 6 days ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
0
votes
2
replies
949
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 29 days ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
0
votes
2
replies
64
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
11 hours ago • updated 8 hours ago
makala
• 0
1
vote
2
replies
259
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 27 days ago
Weiqian
▴ 10
0
votes
2
replies
204
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago
kcarey
• 0
0
votes
2
replies
145
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
27 days ago
prity6459
• 0
0
votes
2
replies
927
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
2
votes
2
replies
209
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
0
votes
2
replies
940
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 1 day ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
1
vote
2
replies
233
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
28 days ago
Le
• 0
0
votes
2
replies
236
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
27 days ago • updated 24 days ago
catv
• 0
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
Kim
• 0
0
votes
2
replies
187
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 24 days ago by
taur.vil
• 0
2
votes
2
replies
221
views
fgsea significant result
fgsea
12 days ago • updated 11 days ago
Chris
▴ 10
1
vote
2
replies
364
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 13 days ago
Kim
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 16 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
2
replies
77
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
3 days ago • updated 2 days ago
Yveto
• 0
2
votes
2
replies
262
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago
zzrammal
• 0
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 1 day ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
2
replies
277
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 27 days ago
isaac.vock
• 0
2
votes
2
replies
230
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago
Chris
▴ 10
1
vote
2
replies
176
views
Error in champ.load(): The following specified files do not exist
ChAMP
29 days ago • updated 28 days ago
Sherin
• 0
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 24 days ago by
Guido Hooiveld
★ 4.0k • written 27 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
156
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
Espresso
• 0
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by
k___
▴ 30
1
vote
2
replies
737
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
29 days ago • updated 20 days ago
Patadù
▴ 10
1
vote
2
replies
247
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
8 days ago • updated 7 days ago
Dylan.Sheerin
• 0
0
votes
1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 28 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
126
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 days ago by
4r-rtg
• 0
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
0
votes
1
reply
95
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
3
votes
1
reply
142
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Sara
• 0
0
votes
1
reply
99
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 9 days ago by
shepherl
3.9k • written 9 days ago by
cyril.dalmasso
• 0
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 20 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
260
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
SSSJec
• 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
c53aba27
• 0
0
votes
1
reply
151
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
sajadahmad41454
• 0
0
votes
1
reply
73
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 2 days ago by
Michael Love
42k • written 3 days ago by
piemmea
• 0
2
votes
1
reply
54
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Sara
• 0
2
votes
1
reply
139
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 days ago by
Michael Love
42k • written 10 days ago by
mat149
▴ 70
0
votes
1
reply
167
views
ATACseq merge peaks
DiffBind
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
i.sudbery
▴ 40
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 28 days ago by
Michael Love
42k • written 28 days ago by
09191919
• 0
0
votes
1
reply
52
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
2 days ago • updated 1 day ago
Bhavya
• 0
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 7 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Dev
• 0
2
votes
1
reply
155
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
e1271094
• 0
194 results • Page
3 of 4
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Awards
• All
Popular Question
to
Chris
▴ 10
Popular Question
to
Guido Hooiveld
★ 4.0k
Scholar
to
Michael Love
42k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
boczniak767
▴ 720
Locations
• All
United States,
just now
Melbourne, Australia,
14 minutes ago
United States,
1 hour ago
The Netherlands,
2 hours ago
India,
2 hours ago
Traffic: 404 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