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 :
rna-seq
•
reset
0
votes
1
reply
36
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
7 hours ago
shaunpeterson
• 0
1
vote
2
replies
255
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
2
votes
3
replies
253
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 29 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
0
votes
1
reply
917
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 5 months ago by
ATpoint
★ 4.1k • written 6.1 years ago by
saad_k6
• 0
0
votes
2
replies
323
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
4
replies
733
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
7 months ago
ar14g12
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
2
votes
3
replies
1.7k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gingergeiger22
• 0
0
votes
3
replies
688
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 8 months ago by
Alice
• 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
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
0
votes
3
replies
710
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 11 months ago by
Michael Love
42k • written 11 months ago by
samuelcjx
• 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.3k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 12 months ago by
Rob
• 0 • written 3.5 years ago by
microPhD
• 0
0
votes
3
replies
876
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
FedeXander
• 0
0
votes
3
replies
730
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
FedeXander
• 0
1
vote
1
reply
1.4k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
SH
• 0
0
votes
1
reply
707
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Cynthia
• 0
2
votes
2
replies
742
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
genome_nerd
• 0
0
votes
1
reply
685
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
15 months ago
Jenny Drnevich
★ 2.0k
1
vote
4
replies
1.0k
views
Nested paired design with covariates in limma
RNA-seq
Nested paired design
limma
updated 15 months ago by
Gordon Smyth
50k • written 4.2 years ago by
ibrahim.akkouh
• 0
4
votes
8
replies
2.2k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 15 months ago by
James W. MacDonald
65k • written 4.0 years ago by
morteza.aslanzadeh
▴ 30
0
votes
1
reply
737
views
Error in DESeqDataSetFromHTSeqCount
DESeq2
RNA-seq
HTseq
DESeqDataSetFromHTSeqCount
updated 17 months ago by
Michael Love
42k • written 18 months ago by
abhay.kanodia
• 0
4
votes
6
replies
6.1k
views
strange results with featureCounts
RNA-seq
featureCounts
total RNA
updated 19 months ago by
snijesh
▴ 20 • written 6.0 years ago by
inah
▴ 10
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
22 months ago • updated 21 months ago
Yang Shi
▴ 10
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
22 months ago
Yang Shi
▴ 10
0
votes
0
replies
887
views
Job:
Computational Biology Contractor - Chinook Therapeutics
Patient_stratification
Multi-omics
RNA-seq
Kidney_Disease
22 months ago
eolson
• 0
2
votes
2
replies
1.0k
views
How to deal with stronger effect by donor than treatment
MDS
RNA-Seq
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
Pei
• 0
3
votes
2
replies
5.1k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
updated 24 months ago by
annamariabugaj
▴ 10 • written 3.8 years ago by
ag1805x
▴ 80
5
votes
5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq
PCA
control
DESeq2
Quality
2.2 years ago • updated 2.0 years ago
9906201a
▴ 20
3
votes
3
replies
3.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER
RNA-seq
differential expression
hidden confounders
updated 2.2 years ago by
ahadli.farid
▴ 30 • written 5.3 years ago by
rodrigo.duarte88
▴ 30
0
votes
2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.2 years ago by
Helen
• 0 • written 6.2 years ago by
tarun2
• 0
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.3 years ago
Lucy
▴ 60
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
samuelcjx
• 0
5
votes
2
replies
22k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 2.3 years ago by
rickap
• 0 • written 5.4 years ago by
aishu.jp
▴ 30
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.3 years ago by
ATpoint
★ 4.1k • written 3.2 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
911
views
First time Statistical Analysis of RNA-seq
edgeR
RNA-Seq
log2
foldchange
q_value
updated 2.3 years ago by
Gordon Smyth
50k • written 2.3 years ago by
johndavidgriner74
• 0
0
votes
7
replies
2.5k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 2.5 years ago by
nicolette.sipperly
• 0 • written 7.0 years ago by
urjaswita
▴ 40
5
votes
12
replies
5.6k
views
DESeq2 time series contrasts between timepoints
rna-seq
deseq2
updated 2.6 years ago by
AZ
▴ 30 • written 6.6 years ago by
gtho123
▴ 40
1
vote
1
reply
2.7k
views
create S-plots with ropls package
s-plot
ropls
opls-da
rna-seq
updated 2.8 years ago by
Nathalie
▴ 10 • written 3.9 years ago by
andreia
▴ 10
0
votes
1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
2.8 years ago
slcno
• 0
0
votes
1
reply
1.5k
views
igraph clustering for gene coexpression network
igraph
network
gene corexpression
rna-seq
updated 2.8 years ago by
Gordon Smyth
50k • written 5.1 years ago by
aiswaryabioinfo
• 0
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.8 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
925
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.8 years ago
lianov
• 0
3
votes
5
replies
2.6k
views
Negative binomial fitting DESeq2
DESeq2
RNA-seq
updated 2.9 years ago by
Michael Love
42k • written 2.9 years ago by
Lucy
▴ 60
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 3.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 3.0 years ago by
mario.keller.1988
▴ 20
0
votes
1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
lkianmehr
• 0
50 results • Page
1 of 1
Recent ...
Replies
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!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
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
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
Popular Question
to
Johannes Rainer
★ 2.0k
Locations
• All
United States,
6 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
United States,
1 hour ago
San Diego,
1 hour ago
Sweden,
2 hours ago
Traffic: 616 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