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
4
replies
375
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by
Ziliang
• 0 • written 18 days ago by
Ian D.
▴ 70
0
votes
3
replies
8.8k
views
SingleR Label.Ont
SingleR
updated 8 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
2
votes
7
replies
384
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
11 days ago • updated 8 days ago
sajadahmad41454
• 0
1
vote
5
replies
518
views
Can't post a question containing code?
Bioconductor
updated 8 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
3
votes
10
replies
457
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
Abbey
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 9 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
169
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
5
votes
3
replies
312
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
271
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
10 days ago • updated 9 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
78
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 10 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
107
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 10 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
3
votes
4
replies
525
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 11 days ago by
Mike Smith
★ 6.5k • written 13 days ago by
robersy
• 0
1
vote
3
replies
304
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 11 days ago by
ATpoint
★ 4.1k • written 17 days ago by
angelathuynh5
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 11 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
3
votes
5
replies
296
views
Help with running egsea()
EGSEA
12 days ago • updated 11 days ago
Chris
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 11 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
0
replies
73
views
Treeio as.treedata function seq lenght error
treeio
11 days ago
nromerov
• 0
4
votes
9
replies
493
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 11 days ago
Juan Higareda
• 0
2
votes
1
reply
173
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
e1271094
• 0
0
votes
1
reply
113
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 12 days ago by
shepherl
3.9k • written 12 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
93
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 12 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
233
views
Couldn't connect to server while using "pathways"
graphite
updated 12 days ago by
Michael Love
42k • written 13 days ago by
fduguchunhui
• 0
4
votes
2
replies
627
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
16 days ago • updated 12 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
150
views
How to save the DEXSeq results
DEXSeq
updated 13 days ago by
Michael Love
42k • written 13 days ago by
Sara
• 0
2
votes
1
reply
143
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 13 days ago by
Michael Love
42k • written 13 days ago by
mat149
▴ 70
1
vote
2
replies
216
views
Improving the design matrices vignette in RNAseq123
RNAseq123
27 days ago • updated 13 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
272
views
package goseq seems to be not available on the latest version of R
goseq
updated 13 days ago by
Gordon Smyth
50k • written 15 days ago by
Patrycja
▴ 20
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 13 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
229
views
fgsea significant result
fgsea
14 days ago • updated 13 days ago
Chris
▴ 10
1
vote
1
reply
191
views
Handling multiple differential expression comparisons
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
Zainab
▴ 10
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Reza
• 0
0
votes
6
replies
297
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 15 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
arfranco
▴ 130
1
vote
2
replies
405
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
Kim
• 0
0
votes
0
replies
140
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago
Chris
▴ 10
1
vote
2
replies
373
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 15 days ago
Kim
• 0
0
votes
0
replies
120
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago
Henry
▴ 10
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
19 days ago • updated 16 days ago
Aurora
• 0
0
votes
0
replies
143
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
24 days ago • updated 16 days ago
glaciya2018
• 0
0
votes
2
replies
214
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
17 days ago • updated 16 days ago
kcarey
• 0
0
votes
1
reply
178
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
z_bahari
• 0
0
votes
1
reply
158
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
c53aba27
• 0
0
votes
0
replies
99
views
flowStats for CyTOF
flowStats
16 days ago
tholmes
• 0
0
votes
2
replies
165
views
DESeq2 v1.35.0
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 16 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
92
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 days ago
yvonneh
• 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 days ago
Ian D.
▴ 70
0
votes
1
reply
134
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 17 days ago by
4r-rtg
• 0
45,670 results • Page
2 of 914
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Locations
• All
Germany,
36 minutes ago
United States,
53 minutes ago
Hong Kong,
1 hour ago
UPF, Barcelona, Spain,
1 hour ago
Israel,
1 hour ago
Traffic: 367 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