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Showing :
RNA-seq
•
reset
0
votes
2
replies
129
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
13 days ago • updated 11 days ago
davca
• 0
0
votes
4
replies
326
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
9 weeks ago • updated 7 weeks ago
ar14g12
• 0
0
votes
2
replies
3.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.4 years ago by
ag1805x
▴ 80
2
votes
3
replies
594
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 11 weeks ago by
Gordon Smyth
49k • written 11 weeks ago by
gingergeiger22
• 0
0
votes
3
replies
408
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 3 months ago by
Alejandro Reyes
★ 1.9k • written 3 months ago by
Alice
• 0
3
votes
4
replies
584
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
3 months ago
Eva
▴ 10
0
votes
3
replies
483
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 5 months ago by
Michael Love
41k • written 5 months ago by
samuelcjx
• 0
5
votes
7
replies
753
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 6 months ago by
Gordon Smyth
49k • written 6 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
513
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 6 months ago by
James W. MacDonald
64k • written 6 months ago by
FedeXander
• 0
0
votes
3
replies
559
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 6 months ago by
James W. MacDonald
64k • written 6 months ago by
FedeXander
• 0
1
vote
1
reply
725
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 7 months ago by
ATpoint
★ 3.6k • written 7 months ago by
SH
• 0
0
votes
1
reply
409
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 8 months ago by
James W. MacDonald
64k • written 8 months ago by
Cynthia
• 0
2
votes
2
replies
513
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 8 months ago by
ATpoint
★ 3.6k • written 8 months ago by
genome_nerd
• 0
0
votes
1
reply
439
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
9 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
552
views
Error in DESeqDataSetFromHTSeqCount
DESeq2
RNA-seq
HTseq
DESeqDataSetFromHTSeqCount
updated 12 months ago by
Michael Love
41k • written 12 months ago by
abhay.kanodia
• 0
5
votes
9
replies
1.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
16 months ago
Yang Shi
▴ 10
2
votes
2
replies
927
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
16 months ago
Yang Shi
▴ 10
0
votes
0
replies
682
views
Job:
Computational Biology Contractor - Chinook Therapeutics
Patient_stratification
Multi-omics
RNA-seq
Kidney_Disease
16 months ago
eolson
• 0
2
votes
2
replies
737
views
How to deal with stronger effect by donor than treatment
MDS
RNA-Seq
updated 16 months ago by
Gordon Smyth
49k • written 16 months ago by
Pei
• 0
0
votes
2
replies
1.7k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 3 months ago by
manuel.fernandez
• 0 • written 20 months ago by
cicely.day
• 0
3
votes
3
replies
2.9k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER
RNA-seq
differential expression
hidden confounders
updated 20 months ago by
ahadli.farid
▴ 30 • written 4.9 years ago by
rodrigo.duarte88
▴ 30
5
votes
5
replies
1.4k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq
PCA
control
DESeq2
Quality
21 months ago • updated 19 months ago
9906201a
▴ 20
1
vote
5
replies
1.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
22 months ago • updated 21 months ago
Lucy
▴ 60
1
vote
3
replies
1.1k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 22 months ago by
Michael Love
41k • written 22 months ago by
samuelcjx
• 0
0
votes
5
replies
2.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 23 months ago by
ATpoint
★ 3.6k • written 2.7 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
777
views
First time Statistical Analysis of RNA-seq
edgeR
RNA-Seq
log2
foldchange
q_value
updated 23 months ago by
Gordon Smyth
49k • written 23 months ago by
johndavidgriner74
• 0
1
vote
1
reply
2.2k
views
create S-plots with ropls package
s-plot
ropls
opls-da
rna-seq
updated 2.3 years ago by
Nathalie
▴ 10 • written 3.4 years ago by
andreia
▴ 10
0
votes
5
replies
1.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.3 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
720
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.4 years ago
lianov
• 0
0
votes
1
reply
807
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
2.4 years ago • updated 2.3 years ago
slcno
• 0
3
votes
5
replies
2.2k
views
Negative binomial fitting DESeq2
DESeq2
RNA-seq
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
Lucy
▴ 60
0
votes
1
reply
1.1k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.5 years ago by
Kevin Blighe
3.9k • written 2.5 years ago by
lkianmehr
• 0
2
votes
3
replies
1.0k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 2.5 years ago by
Gordon Smyth
49k • written 2.5 years ago by
Alex
• 0
5
votes
2
replies
18k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 22 months ago by
rickap
• 0 • written 4.9 years ago by
aishu.jp
▴ 30
1
vote
1
reply
1.5k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 2.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.5 years ago by
mario.keller.1988
▴ 20
3
votes
4
replies
897
views
need help regarding differential expression analysis
rna-seq
updated 2.5 years ago by
Kevin Blighe
3.9k • written 2.5 years ago by
Rishav
▴ 20
0
votes
0
replies
768
views
Job:
Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq
Job
Single-Cell
2.6 years ago
rbrns
• 0
1
vote
4
replies
3.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.2 years ago by
maleknias
• 0
3
votes
4
replies
1.2k
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
2.6 years ago
Antonio M.
• 0
1
vote
2
replies
936
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 2.7 years ago by
Gordon Smyth
49k • written 2.7 years ago by
athief
▴ 20
1
vote
7
replies
1.2k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
2.7 years ago
decppced
• 0
1
vote
3
replies
739
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2
RNA-seq
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
zroger499
• 0
0
votes
0
replies
770
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
2.9 years ago
wrzl
• 0
3
votes
9
replies
1.9k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq
tximeta
3.0 years ago
Pufall, Miles A
▴ 30
0
votes
1
reply
831
views
Limma/Voom Normalized Counts
limma
RNA-seq
updated 3.0 years ago by
Gordon Smyth
49k • written 3.0 years ago by
jackiesalzbank
• 0
0
votes
2
replies
1.2k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester
simulation
RNA-seq
syntheticdata
updated 3.0 years ago by
Gordon Smyth
49k • written 3.0 years ago by
Endre Sebestyén
▴ 70
0
votes
2
replies
1.0k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 6 months ago by
Rob
• 0 • written 3.1 years ago by
microPhD
• 0
3
votes
6
replies
2.5k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion
RNA-seq
DESeq2
Multiple-group
updated 2.8 years ago by
Michael Love
41k • written 3.1 years ago by
Kelen
▴ 10
0
votes
3
replies
1.2k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
Endre Sebestyén
▴ 70
0
votes
3
replies
955
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq
DESeq2
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
julie.green
• 0
50 results • Page
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Answer: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label
by
Peter Hickey
▴ 650
An example usually helps. Here's a way to do it using base R. ``` library(DropletUtils) # Mocking up some 10X HDF5-formatted data. out <-…
Answer: rDGIdb package inconsistency with web interface
by
James W. MacDonald
64k
It doesn't appear to be inconsistent. Here is the [API call result][1]. And the [query on the old version][2]. Although as you may be notin…
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label
by
Peter Hickey
▴ 650
Initially posted to https://github.com/MarioniLab/DropletUtils/issues/104
Comment: How to read fcs3.2 files
by
James W. MacDonald
64k
You need to supply more information than saying you tried things and they didn't work. Show code with error messages.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Looks good then.
Votes
Answer: SingleR annotation of several slots/patients
Answer: List of Deprecated Packages for Bioc3.18
Attempting to import SBML file using R
Answer: RNASeq time course analysis, missing time points for control
Answer: biomaRt not working - lazy table error
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