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1
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2
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154
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
2
votes
2
replies
149
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
7 days ago • updated 6 days ago
julia_mcdonough
• 0
2
votes
2
replies
136
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago
Henry
▴ 10
0
votes
1
reply
110
views
Bioinformatics student
Des
DESeq2
updated 7 days ago by
hemantcnaik
• 0 • written 7 days ago by
Sahar
• 0
0
votes
0
replies
64
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
7 days ago
shepherl
3.8k
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
190
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
5
votes
9
replies
799
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
Chris
• 0
0
votes
0
replies
68
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
7 days ago
Stevie Pederson
• 0
2
votes
2
replies
336
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 days ago • updated 7 days ago
Henry
▴ 10
0
votes
4
replies
181
views
Storing directories inside an ExperimentHub package?
ExperimentHub
9 days ago • updated 8 days ago
Tim Barry
• 0
0
votes
0
replies
73
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
8 days ago
communication
• 0
3
votes
6
replies
210
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
8 days ago
nhaus
▴ 30
0
votes
1
reply
142
views
DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago
Shefali
• 0
0
votes
0
replies
100
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
9 days ago
Eryn
• 0
0
votes
0
replies
68
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
9 days ago
Dennis
• 0
0
votes
1
reply
112
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Lucie
• 0
8
votes
23
replies
767
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 8 days ago by
Robert Castelo
★ 3.2k • written 9 days ago by
Bine
▴ 40
0
votes
1
reply
106
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 9 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Merav
• 0
0
votes
2
replies
180
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 9 days ago by
Michael Love
41k • written 14 days ago by
nhaus
▴ 30
0
votes
1
reply
130
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Adelaide
• 0
0
votes
2
replies
215
views
Regressing out batch effects
DESeq2
updated 9 days ago by
Michael Love
41k • written 15 days ago by
kys91240
• 0
5
votes
6
replies
380
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
0
votes
1
reply
121
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
zh9118
• 0
1
vote
6
replies
428
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
Lucy
▴ 60
0
votes
0
replies
81
views
ggtree tip label position (depth)
ggtree
10 days ago • updated 9 days ago
Roope
• 0
2
votes
6
replies
310
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
11 days ago
Chris
• 0
0
votes
1
reply
146
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
BCS12
• 0
0
votes
0
replies
104
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
11 days ago
arne.sahm
• 0
0
votes
0
replies
73
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
11 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
382
views
Obtaining pheno data from CEL files
GEO
affy
17 days ago • updated 10 days ago
Kurtis
• 0
0
votes
1
reply
139
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
avery
• 0
1
vote
3
replies
220
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
191
views
MethylKit read issue
methylKit
updated 14 days ago by
James W. MacDonald
65k • written 19 days ago by
CHEN
• 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 14 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
4
replies
281
views
Help with design.matrix
limma
14 days ago • updated 13 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
122
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
14 days ago
andromeda
• 0
0
votes
2
replies
132
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
158
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 14 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
108
views
Granges regionCounts not returning the expected number of entries
methylKit
14 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
77
views
flowDensity on a flowset
flowDensity
15 days ago
fredrikwallberg
• 0
1
vote
1
reply
148
views
DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
Hong Thu
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 15 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
190
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 15 days ago by
Tim Peters
▴ 170 • written 16 days ago by
Kim
• 0
0
votes
0
replies
70
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
15 days ago
Macsue
• 0
1
vote
4
replies
398
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 14 days ago by
Gordon Smyth
50k • written 16 days ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 15 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
728
views
error in install immunedeconv
Install
updated 15 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
392
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 15 days ago by
Michael Love
41k • written 16 days ago by
RL
• 0
0
votes
2
replies
162
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago
Gimena
• 0
200 results • Page
2 of 4
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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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