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Votes
2
votes
2
replies
129
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
6 days ago • updated 3 days ago
daniel.carbajo
• 0
0
votes
3
replies
181
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 hours ago by
W. Evan Johnson
▴ 850 • written 6 days ago by
schlumbohm
• 0
5
votes
9
replies
778
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 7 hours ago
Chris
• 0
0
votes
0
replies
67
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 days ago
Stevie Pederson
• 0
2
votes
2
replies
335
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
4
replies
178
views
Storing directories inside an ExperimentHub package?
ExperimentHub
8 days ago • updated 7 days ago
Tim Barry
• 0
0
votes
0
replies
71
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
7 days ago
communication
• 0
3
votes
6
replies
202
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
7 days ago
nhaus
▴ 30
0
votes
1
reply
140
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
0
votes
0
replies
99
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
8 days ago
Eryn
• 0
0
votes
0
replies
67
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
8 days ago
Dennis
• 0
0
votes
1
reply
108
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 8 days ago by
Lucie
• 0
8
votes
23
replies
749
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 7 days ago by
Robert Castelo
★ 3.2k • written 8 days ago by
Bine
▴ 40
0
votes
1
reply
103
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 8 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Merav
• 0
0
votes
2
replies
177
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
41k • written 13 days ago by
nhaus
▴ 30
0
votes
1
reply
126
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 8 days ago by
Michael Love
41k • written 9 days ago by
Adelaide
• 0
0
votes
2
replies
212
views
Regressing out batch effects
DESeq2
updated 8 days ago by
Michael Love
41k • written 14 days ago by
kys91240
• 0
5
votes
6
replies
373
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 days ago by
ATpoint
★ 4.0k • written 9 days ago by
nhaus
▴ 30
0
votes
1
reply
120
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
zh9118
• 0
1
vote
6
replies
426
views
GSVA on separate healthy and disease datasets
GSVA
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
Lucy
▴ 60
0
votes
0
replies
80
views
ggtree tip label position (depth)
ggtree
9 days ago • updated 8 days ago
Roope
• 0
2
votes
6
replies
303
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
10 days ago
Chris
• 0
0
votes
1
reply
145
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
BCS12
• 0
0
votes
0
replies
100
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
10 days ago
arne.sahm
• 0
0
votes
0
replies
72
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
10 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
378
views
Obtaining pheno data from CEL files
GEO
affy
16 days ago • updated 9 days ago
Kurtis
• 0
0
votes
1
reply
136
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 12 days ago by
avery
• 0
1
vote
3
replies
218
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
188
views
MethylKit read issue
methylKit
updated 13 days ago by
James W. MacDonald
65k • written 18 days ago by
CHEN
• 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 13 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
4
replies
279
views
Help with design.matrix
limma
13 days ago • updated 12 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
119
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
13 days ago
andromeda
• 0
0
votes
2
replies
130
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
157
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 13 days ago by
ATpoint
★ 4.0k • written 13 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
106
views
Granges regionCounts not returning the expected number of entries
methylKit
13 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
76
views
flowDensity on a flowset
flowDensity
14 days ago
fredrikwallberg
• 0
1
vote
1
reply
144
views
DESeq2 - Missing values in count matrix
DESeq2
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Hong Thu
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 14 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
187
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 14 days ago by
Tim Peters
▴ 170 • written 15 days ago by
Kim
• 0
0
votes
0
replies
69
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
14 days ago
Macsue
• 0
1
vote
4
replies
397
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 13 days ago by
Gordon Smyth
50k • written 15 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 14 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
727
views
error in install immunedeconv
Install
updated 14 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
391
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 14 days ago by
Michael Love
41k • written 15 days ago by
RL
• 0
0
votes
2
replies
161
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
15 days ago
Gimena
• 0
0
votes
2
replies
138
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
15 days ago
Marianna
▴ 20
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 15 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
283
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 7 days ago by
Tim Peters
▴ 170 • written 16 days ago by
s.malik
• 0
1
vote
1
reply
127
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
16 days ago • updated 15 days ago
Layal
• 0
0
votes
2
replies
204
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
21 days ago • updated 16 days ago
w.cookson
• 0
200 results • Page
2 of 4
Recent ...
Replies
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
sredemption
• 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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