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2
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2
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179
views
[DiffBind] Obtaining normalization factors
DiffBind
4 weeks ago • updated 27 days ago
Henry
▴ 10
0
votes
1
reply
142
views
Bioinformatics student
Des
DESeq2
updated 4 weeks ago by
hemantcnaik
• 0 • written 4 weeks ago by
Sahar
• 0
0
votes
0
replies
92
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
4 weeks ago
shepherl
3.9k
2
votes
2
replies
181
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
4 weeks ago • updated 28 days ago
daniel.carbajo
• 0
0
votes
3
replies
270
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 24 days ago by
W. Evan Johnson
▴ 850 • written 4 weeks ago by
schlumbohm
• 0
5
votes
9
replies
947
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
4 weeks ago • updated 24 days ago
Chris
• 0
0
votes
0
replies
100
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
4 weeks ago
Stevie Pederson
• 0
2
votes
2
replies
405
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
4 weeks ago
Henry
▴ 10
0
votes
4
replies
236
views
Storing directories inside an ExperimentHub package?
ExperimentHub
4 weeks ago
Tim Barry
• 0
0
votes
0
replies
110
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
4 weeks ago
communication
• 0
3
votes
6
replies
297
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
4 weeks ago
nhaus
▴ 30
0
votes
1
reply
190
views
DESeq2 gives an error and R crashes
DESeq2
4 weeks ago
Shefali
• 0
0
votes
0
replies
144
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
4 weeks ago
Eryn
• 0
0
votes
0
replies
90
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
4 weeks ago
Dennis
• 0
0
votes
1
reply
171
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 28 days ago by
Guido Hooiveld
★ 3.9k • written 4 weeks ago by
Lucie
• 0
8
votes
23
replies
1.0k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 4 weeks ago by
Robert Castelo
★ 3.3k • written 4 weeks ago by
Bine
▴ 40
0
votes
1
reply
148
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Merav
• 0
0
votes
2
replies
232
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
nhaus
▴ 30
0
votes
1
reply
177
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Adelaide
• 0
0
votes
2
replies
256
views
Regressing out batch effects
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
kys91240
• 0
5
votes
6
replies
445
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
159
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zh9118
• 0
1
vote
6
replies
514
views
GSVA on separate healthy and disease datasets
GSVA
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Lucy
▴ 60
0
votes
0
replies
118
views
ggtree tip label position (depth)
ggtree
4 weeks ago
Roope
• 0
2
votes
6
replies
438
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
4 weeks ago
Chris
• 0
0
votes
1
reply
185
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
BCS12
• 0
0
votes
0
replies
163
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
4 weeks ago
arne.sahm
• 0
0
votes
0
replies
108
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
4 weeks ago
Wolfgang Huber
★ 13k
1
vote
10
replies
469
views
Obtaining pheno data from CEL files
GEO
affy
5 weeks ago • updated 4 weeks ago
Kurtis
• 0
0
votes
1
reply
179
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
avery
• 0
1
vote
3
replies
270
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
247
views
MethylKit read issue
methylKit
updated 5 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
CHEN
• 0
1
vote
2
replies
3.2k
views
Extract genes from ggvenn?
ggvenn
updated 5 weeks ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
325
views
Help with design.matrix
limma
5 weeks ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
159
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
5 weeks ago
andromeda
• 0
0
votes
2
replies
180
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
joshua.mannheimer
• 0
2
votes
2
replies
212
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
138
views
Granges regionCounts not returning the expected number of entries
methylKit
5 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
110
views
flowDensity on a flowset
flowDensity
5 weeks ago
fredrikwallberg
• 0
1
vote
1
reply
179
views
DESeq2 - Missing values in count matrix
DESeq2
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 5 weeks ago by
Shiva
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 3.9k
1
vote
2
replies
337
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 9 days ago
Kim
• 0
0
votes
0
replies
100
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
5 weeks ago
Macsue
• 0
1
vote
4
replies
454
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 5 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
788
views
error in install immunedeconv
Install
updated 5 weeks ago by
Arash
• 0 • written 14 months ago by
fenglingao
• 0
1
vote
6
replies
452
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
RL
• 0
0
votes
2
replies
200
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
5 weeks ago
Gimena
• 0
0
votes
2
replies
184
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
5 weeks ago
Marianna
▴ 20
2
votes
6
replies
1.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 5 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
1,000 results • Page
4 of 20
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Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
zzrammal
• 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
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