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rna-seq
•
reset
0
votes
1
reply
853
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 3 months ago by
ATpoint
★ 3.9k • written 5.9 years ago by
saad_k6
• 0
0
votes
2
replies
263
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
3 months ago
davca
• 0
0
votes
4
replies
599
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
5 months ago
ar14g12
• 0
0
votes
2
replies
3.4k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.7 years ago by
ag1805x
▴ 80
2
votes
3
replies
1.3k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
gingergeiger22
• 0
0
votes
3
replies
591
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 6 months ago by
Alejandro Reyes
★ 1.9k • written 6 months ago by
Alice
• 0
3
votes
4
replies
780
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
7 months ago
Eva
▴ 10
0
votes
3
replies
608
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 9 months ago by
Michael Love
41k • written 9 months ago by
samuelcjx
• 0
5
votes
7
replies
1.1k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
644
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 10 months ago by
James W. MacDonald
65k • written 10 months ago by
FedeXander
• 0
0
votes
3
replies
787
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
FedeXander
• 0
1
vote
1
reply
1.1k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 11 months ago by
ATpoint
★ 3.9k • written 11 months ago by
SH
• 0
0
votes
1
reply
623
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Cynthia
• 0
2
votes
2
replies
655
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 11 months ago by
ATpoint
★ 3.9k • written 12 months ago by
genome_nerd
• 0
0
votes
1
reply
596
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
13 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
655
views
Error in DESeqDataSetFromHTSeqCount
DESeq2
RNA-seq
HTseq
DESeqDataSetFromHTSeqCount
updated 15 months ago by
Michael Love
41k • written 16 months ago by
abhay.kanodia
• 0
5
votes
9
replies
1.7k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
20 months ago • updated 19 months ago
Yang Shi
▴ 10
2
votes
2
replies
1.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
20 months ago
Yang Shi
▴ 10
0
votes
0
replies
809
views
Job:
Computational Biology Contractor - Chinook Therapeutics
Patient_stratification
Multi-omics
RNA-seq
Kidney_Disease
20 months ago
eolson
• 0
2
votes
2
replies
905
views
How to deal with stronger effect by donor than treatment
MDS
RNA-Seq
updated 20 months ago by
Gordon Smyth
50k • written 20 months ago by
Pei
• 0
0
votes
2
replies
2.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 6 months ago by
manuel.fernandez
• 0 • written 23 months ago by
cicely.day
• 0
3
votes
3
replies
3.2k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER
RNA-seq
differential expression
hidden confounders
updated 2.0 years ago by
ahadli.farid
▴ 30 • written 5.2 years ago by
rodrigo.duarte88
▴ 30
5
votes
5
replies
1.5k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq
PCA
control
DESeq2
Quality
2.1 years ago • updated 22 months ago
9906201a
▴ 20
1
vote
5
replies
1.8k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.1 years ago
Lucy
▴ 60
1
vote
3
replies
1.3k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
samuelcjx
• 0
0
votes
5
replies
3.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.2 years ago by
ATpoint
★ 3.9k • written 3.0 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
857
views
First time Statistical Analysis of RNA-seq
edgeR
RNA-Seq
log2
foldchange
q_value
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
johndavidgriner74
• 0
1
vote
1
reply
2.5k
views
create S-plots with ropls package
s-plot
ropls
opls-da
rna-seq
updated 2.6 years ago by
Nathalie
▴ 10 • written 3.7 years ago by
andreia
▴ 10
0
votes
5
replies
1.1k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.6 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
846
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.6 years ago
lianov
• 0
0
votes
1
reply
945
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
2.7 years ago • updated 2.6 years ago
slcno
• 0
3
votes
5
replies
2.4k
views
Negative binomial fitting DESeq2
DESeq2
RNA-seq
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
Lucy
▴ 60
0
votes
1
reply
1.4k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
lkianmehr
• 0
2
votes
3
replies
1.1k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 2.8 years ago by
Gordon Smyth
50k • written 2.8 years ago by
Alex
• 0
5
votes
2
replies
20k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 2.1 years ago by
rickap
• 0 • written 5.2 years ago by
aishu.jp
▴ 30
1
vote
1
reply
1.6k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 2.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.8 years ago by
mario.keller.1988
▴ 20
3
votes
4
replies
1.0k
views
need help regarding differential expression analysis
rna-seq
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Rishav
▴ 20
0
votes
0
replies
866
views
Job:
Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq
Job
Single-Cell
2.8 years ago
rbrns
• 0
1
vote
4
replies
3.6k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 2.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.5 years ago by
maleknias
• 0
3
votes
4
replies
1.3k
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
2.9 years ago
Antonio M.
• 0
1
vote
2
replies
1.0k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
athief
▴ 20
1
vote
7
replies
1.3k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
3.0 years ago
decppced
• 0
1
vote
3
replies
811
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2
RNA-seq
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
zroger499
• 0
0
votes
0
replies
843
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
3.1 years ago
wrzl
• 0
3
votes
9
replies
2.1k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq
tximeta
3.3 years ago
Pufall, Miles A
▴ 30
0
votes
1
reply
973
views
Limma/Voom Normalized Counts
limma
RNA-seq
updated 3.3 years ago by
Gordon Smyth
50k • written 3.3 years ago by
jackiesalzbank
• 0
0
votes
2
replies
1.4k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester
simulation
RNA-seq
syntheticdata
updated 3.3 years ago by
Gordon Smyth
50k • written 3.3 years ago by
Endre Sebestyén
▴ 70
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 10 months ago by
Rob
• 0 • written 3.4 years ago by
microPhD
• 0
3
votes
6
replies
2.8k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion
RNA-seq
DESeq2
Multiple-group
updated 3.1 years ago by
Michael Love
41k • written 3.4 years ago by
Kelen
▴ 10
0
votes
3
replies
1.3k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 3.4 years ago by
Robert Castelo
★ 3.1k • written 3.4 years ago by
Endre Sebestyén
▴ 70
50 results • Page
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Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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