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
9
replies
3.5k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
2.7 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.1k
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
m-bihie
▴ 10
0
votes
1
reply
1.6k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Cynthia
• 0
2
votes
2
replies
1.3k
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
genome_nerd
• 0
0
votes
1
reply
777
views
How to adjust plots generated using psygenet2r?
psygenet2r
updated 2.7 years ago by
helucro
▴ 70 • written 2.7 years ago by
marinaw
▴ 20
0
votes
2
replies
1.1k
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 2.7 years ago by
pmadrigal
• 0 • written 2.7 years ago by
Kritikaverma2707
• 0
3
votes
2
replies
1.5k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2
apeglm
2.7 years ago
Daphnia
• 0
0
votes
2
replies
2.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
2
votes
1
reply
4.2k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
Chris
▴ 20
2
votes
3
replies
3.7k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
0
votes
0
replies
837
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
2.7 years ago
garbuzov
• 0
0
votes
0
replies
796
views
Plot profiles for each group - spline analysis in edgeR
timecoursedata
edgeR
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
boczniak767
▴ 740
0
votes
2
replies
1.2k
views
Compare and filter three BAM files
RNAseq
10X
2.7 years ago
wt215
• 0
1
vote
1
reply
993
views
FlowSOM with unrelated channels
FlowSOM
cytofWorkflow
updated 2.7 years ago by
helucro
▴ 70 • written 2.7 years ago by
Anirban
• 0
0
votes
0
replies
806
views
Module Trait Corelation
WGCNA
2.7 years ago
allanokwaro
• 0
0
votes
1
reply
1.5k
views
Specific versions of packages
Bioconductor
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Gábor Csárdi
▴ 90
1
vote
1
reply
2.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 2.7 years ago by
Cynthia
• 0 • written 2.7 years ago by
Nargil
• 0
0
votes
13
replies
13k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
2.7 years ago
Laia
▴ 10
3
votes
1
reply
876
views
How edgeR estimate the common dispersion?
edgeR
2.8 years ago • updated 2.7 years ago
Dan
• 0
0
votes
6
replies
1.2k
views
DispEsts plot
DESeq2
2.7 years ago
Sep
• 0
0
votes
0
replies
720
views
getGEO error when trying to download a series matrix file
getGEOerror
2.7 years ago
suyonj
• 0
1
vote
3
replies
1.5k
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
2.7 years ago
rmoorehe
• 0
0
votes
1
reply
791
views
Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
S
• 0
0
votes
0
replies
646
views
Align to reference genome
Alignment
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Antonio
• 0
4
votes
4
replies
1.6k
views
Can I run DESeq2 with SMART-Seq data
DESeq2
SMART-seq
2.7 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
6.2k
views
How to change the dot size in plotPCA?
plotPCA
PCA
updated 2.7 years ago by
hediatnani
• 0 • written 2.7 years ago by
Yijing
• 0
0
votes
5
replies
2.3k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 2.7 years ago by
andrewsm
• 0
0
votes
1
reply
972
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
fuqichen1
• 0
0
votes
3
replies
1.3k
views
How to getting synonymous SNPs from BiomaRt before timing out?
biomaRt
SNP
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Damien
• 0
0
votes
0
replies
1.3k
views
News:
Bioconductor 3.17 db0s, OrgDbs, and TxDbs now available
release
db0
Annotation
2.7 years ago
kayla.interdonato
▴ 160
2
votes
1
reply
807
views
Are polynomial contrasts for a time factor possible in DESeq2?
DESeq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
dairey
▴ 10
1
vote
7
replies
4.8k
views
MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
msa
MultipleSequenceAlignment
updated 2.7 years ago by
stitam
• 0 • written 4.7 years ago by
thanos_docp
• 0
0
votes
1
reply
801
views
deseq2 nested multifactorial analysis
DESeq2
multifactorial
nested
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
jd
• 0
0
votes
0
replies
803
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
2.7 years ago
edward.esiribloom
• 0
0
votes
4
replies
118k
views
Unable to create venndiagram using VennDiagram 1.5.1 package
updated 2.7 years ago by
konstantinernst
• 0 • written 13.1 years ago by
jay kumar
▴ 10
0
votes
1
reply
931
views
Limma for Fluidigm high throughput PCR
limma
Limma
Fluidigm
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
jms2520
▴ 10
1
vote
4
replies
2.7k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
Yang Shi
▴ 10
2
votes
1
reply
5.5k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 2.7 years ago by
RMiller
▴ 20 • written 2.7 years ago by
kevin
• 0
0
votes
0
replies
1.0k
views
Human to mouse SNP conversion
liftOver
SNP
GWASTools
2.7 years ago
bonheur
• 0
0
votes
2
replies
1.0k
views
Help understanding dispersion values and why so many genes change significance after removing low read samples
DESeq2
2.7 years ago
Miriam
• 0
6
votes
6
replies
10k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 14 months ago by
wl_xxz
• 0 • written 2.7 years ago by
luca.s
▴ 50
3
votes
20
replies
3.7k
views
Time-course, comparison of two groups
edgeR
2.7 years ago
boczniak767
▴ 740
0
votes
1
reply
2.2k
views
DESeqDataSetFromMatrix NA values
DESeq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
hyejo
• 0
2
votes
0
replies
1.4k
views
Job:
Postdoc at EMBL: spatial and single-cell computational biology for precision oncology, based in Heidelberg, Germany
omics
Spatial
postdoc
2.7 years ago
Wolfgang Huber
★ 13k
1
vote
3
replies
1.3k
views
How to compute(calculate) rlog and vst provided from DESeq2
DESeq2
2.7 years ago
tstpp
• 0
0
votes
1
reply
773
views
Outlier removal outcome
Outlier
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
sanchita.bhattacharya
• 0
4
votes
8
replies
3.0k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID
TxDB.Hsapiens.UCSC.hg38.knownGene
locateVariants
GenomicFeatures
VariantAnnotation
2.7 years ago
davidhillis
• 0
2
votes
7
replies
1.7k
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
Constantin Ahlmann-Eltze
▴ 40
1
vote
2
replies
757
views
DESeq2 pvalues overly conservative
DESeq2
2.7 years ago
gdolsten
▴ 10
46,691 results • Page
57 of 934
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
James W. MacDonald
68k
Popular Question
to
Gordon Smyth
53k
Commentator
to
sina.nassiri
▴ 130
Popular Question
to
Hervé Pagès
16k
Popular Question
to
jared.andrews07
▴ 30
Locations
• All
Pakistan,
6 minutes ago
United States,
1 hour ago
United States,
1 hour ago
United States,
2 hours ago
United States,
2 hours ago
Traffic: 981 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