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1.1k
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[DiffBind] Obtaining normalization factors
DiffBind
20 months ago
Henry
▴ 10
0
votes
1
reply
646
views
Bioinformatics student
Des
DESeq2
updated 20 months ago by
hemantcnaik
• 0 • written 20 months ago by
Sahar
• 0
0
votes
0
replies
843
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
21 months ago
shepherl
4.2k
2
votes
2
replies
1.5k
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
21 months ago • updated 20 months ago
daniel.carbajo
• 0
0
votes
3
replies
1.8k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 20 months ago by
W. Evan Johnson
▴ 870 • written 21 months ago by
schlumbohm
• 0
5
votes
9
replies
2.3k
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 months ago • updated 20 months ago
Chris
▴ 20
0
votes
0
replies
615
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 months ago
Stevie Pederson
• 0
2
votes
2
replies
1.8k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
21 months ago • updated 20 months ago
Henry
▴ 10
0
votes
4
replies
875
views
Storing directories inside an ExperimentHub package?
ExperimentHub
21 months ago
Tim Barry
• 0
0
votes
0
replies
559
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
21 months ago
communication
• 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 months ago
nhaus
▴ 70
0
votes
1
reply
784
views
DESeq2 gives an error and R crashes
DESeq2
21 months ago
Shefali
• 0
0
votes
0
replies
855
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 months ago
Eryn
• 0
0
votes
0
replies
510
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
21 months ago
Dennis
• 0
0
votes
2
replies
2.9k
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 months ago by
Andrea
• 0 • written 21 months ago by
Lucie
• 0
8
votes
23
replies
6.2k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 21 months ago by
Robert Castelo
★ 3.4k • written 21 months ago by
Bine
▴ 50
0
votes
1
reply
1.0k
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Merav
• 0
0
votes
2
replies
864
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 21 months ago by
Michael Love
43k • written 21 months ago by
nhaus
▴ 70
0
votes
1
reply
901
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Adelaide
• 0
0
votes
2
replies
780
views
Regressing out batch effects
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
kys91240
• 0
5
votes
6
replies
1.6k
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 21 months ago by
nhaus
▴ 70
0
votes
1
reply
723
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
zh9118
• 0
1
vote
6
replies
1.6k
views
GSVA on separate healthy and disease datasets
GSVA
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Lucy
▴ 60
0
votes
0
replies
1.0k
views
ggtree tip label position (depth)
ggtree
21 months ago
Roope
• 0
2
votes
6
replies
4.4k
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
21 months ago
Chris
▴ 20
0
votes
1
reply
642
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
BCS12
• 0
0
votes
0
replies
982
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
21 months ago
arne.sahm
• 0
0
votes
0
replies
598
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
21 months ago
Wolfgang Huber
★ 13k
1
vote
10
replies
2.0k
views
Obtaining pheno data from CEL files
GEO
affy
21 months ago
Kurtis
• 0
0
votes
1
reply
617
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
avery
• 0
1
vote
3
replies
954
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
1.6k
views
MethylKit read issue
methylKit
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
CHEN
• 0
1
vote
2
replies
5.4k
views
Extract genes from ggvenn?
ggvenn
updated 21 months ago by
Michael
▴ 10 • written 3.7 years ago by
axe880
• 0
0
votes
4
replies
935
views
Help with design.matrix
limma
21 months ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
748
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
21 months ago
andromeda
• 0
0
votes
2
replies
1.1k
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
joshua.mannheimer
• 0
2
votes
2
replies
984
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
642
views
Granges regionCounts not returning the expected number of entries
methylKit
21 months ago
Modoc Kesner
▴ 10
0
votes
0
replies
426
views
flowDensity on a flowset
flowDensity
21 months ago
fredrikwallberg
• 0
1
vote
1
reply
876
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Hong Thu
• 0
10
votes
41
replies
10k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 19 months ago by
Daniele
• 0 • written 7.1 years ago by
Guido Hooiveld
★ 4.1k
1
vote
3
replies
3.1k
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 15 months ago by
rania.alanany
• 0 • written 21 months ago by
Kim
• 0
0
votes
0
replies
696
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
21 months ago
Macsue
• 0
1
vote
4
replies
1.1k
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
jari.karppinen
• 0
3
votes
3
replies
16k
views
How to fix 'long vectors not supported yet' error in R
r
updated 21 months ago by
Amruta
• 0 • written 6.9 years ago by
r.tor
• 0
0
votes
2
replies
2.1k
views
error in install immunedeconv
Install
updated 21 months ago by
Arash
• 0 • written 2.8 years ago by
fenglingao
• 0
1
vote
6
replies
1.7k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 21 months ago by
Michael Love
43k • written 21 months ago by
RL
• 0
0
votes
2
replies
917
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
21 months ago
Gimena
• 0
0
votes
2
replies
971
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
21 months ago
Marianna
▴ 20
1
vote
6
replies
1.8k
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 months ago by
Tim Peters
▴ 230 • written 21 months ago by
s.malik
• 0
46,704 results • Page
27 of 935
Recent ...
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Answer: Guitar R package requires update due to dependency GenomicFeatures
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Kevin Blighe
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Greetings, This issue is indeed caused by recent changes in the Bioconductor 3.20+ release cycle. The function makeTxDbFromGFF() was previ…
Answer: ATACseq rudimentary questions
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For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
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