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RNA-Seq
•
reset
0
votes
1
reply
39
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
9 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
9 days ago • updated 8 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
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
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Alex
• 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
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
3
votes
4
replies
1.1k
views
need help regarding differential expression analysis
rna-seq
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
Rishav
▴ 20
0
votes
0
replies
961
views
Job:
Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq
Job
Single-Cell
3.0 years ago
rbrns
• 0
1
vote
4
replies
3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 3.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
maleknias
• 0
3
votes
4
replies
1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
3.1 years ago
Antonio M.
• 0
1
vote
2
replies
1.1k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
athief
▴ 20
1
vote
7
replies
1.4k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
3.2 years ago
decppced
• 0
1
vote
3
replies
858
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2
RNA-seq
updated 3.2 years ago by
Michael Love
42k • written 3.2 years ago by
zroger499
• 0
0
votes
0
replies
886
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
3.3 years ago
wrzl
• 0
3
votes
9
replies
2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq
tximeta
3.4 years ago
Pufall, Miles A
▴ 30
0
votes
1
reply
1.1k
views
Limma/Voom Normalized Counts
limma
RNA-seq
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
jackiesalzbank
• 0
50 results • Page
1 of 1
Recent ...
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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
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