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135
views
[DiffBind] Obtaining normalization factors
DiffBind
6 days ago • updated 3 days ago
Henry
▴ 10
0
votes
1
reply
109
views
Bioinformatics student
Des
DESeq2
updated 6 days ago by
hemantcnaik
• 0 • written 6 days ago by
Sahar
• 0
2
votes
2
replies
135
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago
daniel.carbajo
• 0
0
votes
3
replies
189
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 hours ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
5
votes
9
replies
796
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
Chris
• 0
2
votes
2
replies
336
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 days ago • updated 6 days ago
Henry
▴ 10
0
votes
1
reply
110
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 8 days ago by
Lucie
• 0
5
votes
6
replies
377
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.0k • written 9 days ago by
nhaus
▴ 30
6
votes
5
replies
374
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
0
votes
5
replies
293
views
DESeq filtering specific to contrasts
DESeq2
updated 11 minutes ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
553
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 2 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 1 day ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
0
votes
4
replies
2.8k
views
SingleR Label.Ont
SingleR
updated 3 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 1 day ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
1
vote
2
replies
750
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 18 hours ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 6 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 1 hour ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 1 day ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
3
votes
1
reply
733
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.1 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
2
replies
886
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
5
votes
13
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
649
views
DESeq2 setting significant p-value
DESeq2
updated 10 minutes ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 5 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 23 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 16 hours ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
76 results • Page
2 of 2
Recent ...
Replies
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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