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
Showing :
RnaSeq
•
reset
2
votes
4
replies
1.1k
views
RNA Seq Analytic Design
rnaseq
deseq2
9.1 years ago
lauren.fitch
• 0
1
vote
6
replies
6.5k
views
How to perform multiple pairwise comparisons
deseq2
bioconductor
rnaseq
updated 2.9 years ago by
Michael Love
43k • written 9.2 years ago by
pkachroo
▴ 10
0
votes
5
replies
11k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 20 months ago by
Eva
• 0 • written 9.2 years ago by
ctl
• 0
1
vote
3
replies
1.8k
views
Interaction term analysis using ballgown
ballgown
stringtie
voom limma
differential gene expression
rnaseq
updated 9.2 years ago by
Alyssa Frazee
▴ 210 • written 9.2 years ago by
jcalis
▴ 10
0
votes
3
replies
3.6k
views
Fisher exact test
rnaseq
differential gene expression
updated 9.2 years ago by
davide risso
▴ 980 • written 9.2 years ago by
elhamdallalbashi
• 0
2
votes
23
replies
5.2k
views
Coping with a label/class imbalance in DESeq2
deseq2
rnaseq
r
regression
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
bkellman
• 0
0
votes
1
reply
1.7k
views
FeatureCounts Assertion `l_name < 100' failed.
featurecounts
rnaseq
9.2 years ago
shg018
• 0
0
votes
1
reply
1.3k
views
Gviz error after updating R
software error
Gviz
chipseq
rnaseq
9.2 years ago
ta_awwad
▴ 10
6
votes
3
replies
1.5k
views
How to deal with these data with DESeq2 ?? In hurry!
deseq2
normalization
rnaseq
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
alanzxr
• 0
0
votes
13
replies
5.1k
views
DESeq2: collapseReplicates error
deseq2
rnaseq
differential gene expression
9.2 years ago
ta_awwad
▴ 10
1
vote
13
replies
16k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
9.2 years ago
yjliu1127
• 0
0
votes
5
replies
2.1k
views
Can Normalized cpm values be used as RUVs input
rnaseq
ruvseq
updated 9.2 years ago by
davide risso
▴ 980 • written 9.2 years ago by
sooby
• 0
0
votes
5
replies
4.4k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
jbatsx
• 0
8
votes
8
replies
5.0k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq
single cell
normalization
edgeR
deseq2
updated 9.2 years ago by
Aaron Lun
★ 29k • written 9.2 years ago by
kieranrcampbell
▴ 50
4
votes
4
replies
3.2k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor
edgeR
design and contrast matrix
rnaseq
differential gene expression
updated 9.2 years ago by
Aaron Lun
★ 29k • written 9.2 years ago by
lidixu.se
• 0
0
votes
0
replies
1.5k
views
Error in SAMseq analysis with R
r
samseq
microarray
rnaseq
geneexpression
9.2 years ago
namilio
• 0
0
votes
10
replies
5.9k
views
Differential expression analysis for STAR-aligned RNA-Seq data
deseq2
rnaseq
STAR
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
sum31278
• 0
1
vote
0
replies
2.0k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq
rna-seq
preprocessing
gsva
9.3 years ago
t.kuilman
▴ 170
3
votes
6
replies
2.5k
views
Clarification MAplot and FDR in EdgeR
edgeR
MAplot
rnaseq
differential gene expression
updated 9.3 years ago by
Gordon Smyth
53k • written 9.3 years ago by
joseph.bergenstrahle
• 0
1
vote
7
replies
3.8k
views
RNA-seq: two factor anova - how to find the variability explained by each of the factor?
rnaseq
two factor anova
limma
DEseq2
edgeR
9.3 years ago
nooshin
▴ 300
1
vote
2
replies
1.9k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
9.3 years ago
joanito.liberti
• 0
4
votes
2
replies
3.8k
views
WGCNA blockwiseModules parallelisation question
wgcna
rnaseq
updated 9.3 years ago by
Peter Langfelder
★ 3.0k • written 9.3 years ago by
caitlin
▴ 10
0
votes
2
replies
1.6k
views
topgo rnaseq error
topgo
rnaseq
9.3 years ago
tarek.mohamed
▴ 10
0
votes
2
replies
3.0k
views
topGO fro RNA-seq
topgo
rnaseq
9.3 years ago
tarek.mohamed
▴ 10
3
votes
6
replies
2.0k
views
Mutation effect on expression (RNA-Seq) using limma
limma
rnaseq
mutations
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 years ago by
Nicolas Rosewick
▴ 20
3
votes
5
replies
5.0k
views
DESeq2 3-fatcor design and different interaction terms
deseq2
bioconductor
rnaseq
multifactorial design
interactions
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
c.evang
▴ 10
2
votes
2
replies
1.3k
views
Ballgown Custom Model Question
ballgown
rnaseq
updated 9.3 years ago by
Jeff Leek
▴ 650 • written 9.3 years ago by
daniel.gaston
• 0
5
votes
4
replies
2.7k
views
Why does the filtering of lowly expressed genes for analysis with edgeR must be done unsupervised?
edgeR
RNAseq
DE analysis
gene filtering
9.3 years ago
Mau
▴ 50
1
vote
2
replies
1.4k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2
featurecounts
rnaseq
updated 9.3 years ago by
James W. MacDonald
68k • written 9.3 years ago by
EJ
▴ 20
3
votes
4
replies
2.1k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 9.3 years ago by
Gordon Smyth
53k • written 9.3 years ago by
thomas.dobrenel
• 0
8
votes
3
replies
1.9k
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 9.3 years ago by
Gordon Smyth
53k • written 9.3 years ago by
rubi
▴ 110
1
vote
1
reply
2.3k
views
Using pathview with uncommon species leads to Errors
pathview
Kegg
rnaseq
data visualization
updated 9.3 years ago by
Luo Weijun
★ 1.6k • written 9.3 years ago by
rafre
• 0
11
votes
9
replies
5.8k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 9.3 years ago by
Gordon Smyth
53k • written 9.3 years ago by
yi.huang
▴ 30
1
vote
4
replies
1.8k
views
Polyester and mutations
rnaseq
pair-end reads
mutations
updated 9.4 years ago by
Jeff Leek
▴ 650 • written 9.4 years ago by
H.Hasani
• 0
0
votes
0
replies
1.3k
views
CummeRbund Expression Bar Plot
cummerbund
rnaseq
9.4 years ago
k1064622
• 0
4
votes
16
replies
9.4k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 20 months ago by
Shaimaa Gamal
• 0 • written 10.5 years ago by
Pauly Lin
▴ 160
3
votes
1
reply
6.6k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger
rnaseq
glm
glmfit
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
alessia.donato
• 0
11
votes
7
replies
8.1k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 9.4 years ago by
Ryan C. Thompson
★ 7.9k • written 9.4 years ago by
kjo
▴ 70
1
vote
1
reply
1.4k
views
Generating ExpressionSet Objects
r
expressionset
subseq
rnaseq
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
rrcutler
▴ 70
0
votes
1
reply
1.6k
views
why my resultsNames(deseq) is not the same as model.matrix ?
deseq2
RNASeq
SVA
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
unique379
• 0
2
votes
1
reply
1.9k
views
polyester: adding noise to RNASeq counts?
rnaseq
polyester
updated 9.4 years ago by
Alyssa Frazee
▴ 210 • written 9.4 years ago by
krishna312
• 0
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
written 9.5 years ago by
alireza_sharifian_10
▴ 20
3
votes
4
replies
10k
views
DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet
DESeqDataSetFromMatrix
rnaseq
deseq2
9.4 years ago
ErickF
▴ 40
4
votes
3
replies
3.4k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps
rnaseq
bplapply
rangedsummarizedexperiment
read counting
9.4 years ago
ErickF
▴ 40
0
votes
2
replies
1.4k
views
Runing into error while trying GRanges from R
rnaseq
bumphunter
genomicranges
9.4 years ago
alva.james
• 0
15
votes
4
replies
3.7k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 9.4 years ago by
Ryan C. Thompson
★ 7.9k • written 9.4 years ago by
WouterDeCoster
▴ 130
14
votes
5
replies
9.0k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 3.6 years ago by
Sarah
• 0 • written 9.4 years ago by
kaihami
▴ 40
1
vote
4
replies
2.3k
views
Effect of treatment vs control over time in RNA Seq (edgeR and limma)
edgeR
limma
voom
RNASeq
multiple time points
updated 9.4 years ago by
Ryan C. Thompson
★ 7.9k • written 9.4 years ago by
joelrome88
▴ 20
2
votes
1
reply
1.6k
views
Affy loess normalization of RNA-seq data
affy
RNAseq
loess
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
JW
• 0
0
votes
3
replies
1.0k
views
DESeq2 analysis returns 41% low count genes
deseq2
rnaseq
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
tarek.mohamed
▴ 10
1,410 results • Page
20 of 29
Recent ...
Replies
Answer: How can I correctly use phyloseq with Docker?
by
Kevin Blighe
★ 4.0k
The Bioconductor version must be compatible with the R version. Bioconductor version 3.18 is compatible with R version 4.3. The Dockerfile …
Answer: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
by
Kevin Blighe
★ 4.0k
Your proposed code is correct and will achieve the desired outcome. The boolean filter expression `IFNg & TNFa | IFNg & IL2 | TNFa & IL2` i…
Answer: Install old version of DESeq2
by
Kevin Blighe
★ 4.0k
The Dockerfile that you have provided is appropriate for installing DESeq2 and apeglm from Bioconductor release 3.10, which corresponds to …
Answer: Guidance Requested on GCN Network Analysis and Module Enrichment in R
by
Kevin Blighe
★ 4.0k
The discrepancy between `final_exp1` and `final_exp2` could arise from several factors, despite matching dimensions. The `identical()` func…
Answer: ORFik: spliced 5utr regions
by
Kevin Blighe
★ 4.0k
Hello Luna. The findUORFs function in ORFik identifies upstream open reading frames by extracting and concatenating the sequences of exo…
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards
• All
Scholar
to
Gordon Smyth
53k
Popular Question
to
shepherl
4.2k
Supporter
to
fabio.marroni
• 0
Popular Question
to
Guido Hooiveld
★ 4.1k
Popular Question
to
James W. MacDonald
68k
Locations
• All
The city by the bay,
1 hour ago
Saudi Arabia,
1 hour ago
The Cave, 181 Longwood Avenue, Boston, USA,
2 hours ago
United States,
3 hours ago
United States,
3 hours ago
Traffic: 960 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