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
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by
Maryam.sed1400
• 0
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 180 • written 7.2 years ago by
Jenny Drnevich
★ 2.0k
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
luis.franco
• 0
2
votes
11
replies
972
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 7 months ago by
cinzia.spagnoli
• 0
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
0
votes
11
replies
796
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
mico
• 0
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 10 months ago by
Gordon Smyth
50k • written 11 months ago by
alexia.brunel
• 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 12 months ago by
Aung
• 0 • written 14 months ago by
pedro-marra
▴ 10
1
vote
11
replies
3.7k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 9 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by
James W. MacDonald
65k • written 20 months ago by
ignadb
• 0
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
6
votes
11
replies
1.1k
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago
gernophil
• 0
9
votes
11
replies
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 9 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 3.3 years ago by
Alberto
• 0
3
votes
11
replies
2.6k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
11 months ago
Anna
▴ 20
0
votes
11
replies
2.1k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.7 years ago by
mike Ad.
▴ 30
3
votes
10
replies
2.8k
views
error in package GenVisR while installing
GenVisR
GenVis
updated 6 months ago by
zlskidmore
▴ 30 • written 22 months ago by
abhisikta
• 0
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 18 months ago by
Alexandros
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 5 weeks ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
0
votes
10
replies
849
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
6 months ago • updated 11 weeks ago
ScafioRuo
• 0
0
votes
10
replies
2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
2
votes
10
replies
3.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by
Michael Love
42k • written 5.8 years ago by
andrebolerbarros
▴ 20
11
votes
10
replies
7.4k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 8 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 20
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
10
replies
856
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
cjag
• 0
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.9k • written 20 months ago by
Florian Finkernagel
▴ 30
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
10
replies
478
views
Obtaining pheno data from CEL files
GEO
affy
6 weeks ago • updated 5 weeks ago
Kurtis
• 0
2
votes
10
replies
1.4k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
15753563659
▴ 50
3
votes
10
replies
463
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
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 12 months ago by
IUH
• 0 • written 6.9 years ago by
stan
• 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
9 months ago
15753563659
▴ 50
1
vote
9
replies
3.0k
views
DEGreport installation help
DEGreport
updated 8 months ago by
James W. MacDonald
65k • written 19 months ago by
marinaw
▴ 20
4
votes
9
replies
1.4k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 9 months ago by
dbunis
▴ 10 • written 9 months ago by
nina.hahn
▴ 10
0
votes
9
replies
707
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago
nromerov
• 0
0
votes
9
replies
863
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
9 months ago • updated 8 months ago
hayleyw
• 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 6 months ago by
Erqiang Hu
▴ 50 • written 6 months ago by
jovel_juan
▴ 30
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.6 years ago by
bharata1803
▴ 60
0
votes
9
replies
592
views
limma fo continous variables
limma
DEGseq
updated 11 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
mia
• 0
2
votes
9
replies
1.8k
views
How to load fasta file with openPrimeR?
openPrimeR
written 3.3 years ago by
marongiu.luigi
• 0
4
votes
9
replies
493
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 12 days ago
Juan Higareda
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
4
votes
9
replies
252
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 9 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards
• All
Popular Question
to
euge.eugenio
▴ 20
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
Locations
• All
United Kingdom,
3 minutes ago
Belgium,
4 minutes ago
Slovakia,
15 minutes ago
United States,
43 minutes ago
United States,
55 minutes ago
Traffic: 382 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