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Votes
2
votes
2
replies
183
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
18 days ago
julia_mcdonough
• 0
2
votes
2
replies
159
views
[DiffBind] Obtaining normalization factors
DiffBind
18 days ago • updated 14 days ago
Henry
▴ 10
0
votes
1
reply
125
views
Bioinformatics student
Des
DESeq2
updated 18 days ago by
hemantcnaik
• 0 • written 18 days ago by
Sahar
• 0
0
votes
0
replies
77
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
18 days ago
shepherl
3.8k
2
votes
2
replies
161
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
18 days ago • updated 16 days ago
daniel.carbajo
• 0
0
votes
3
replies
241
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 12 days ago by
W. Evan Johnson
▴ 850 • written 18 days ago by
schlumbohm
• 0
5
votes
9
replies
890
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
20 days ago • updated 12 days ago
Chris
• 0
0
votes
0
replies
84
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
18 days ago
Stevie Pederson
• 0
2
votes
2
replies
374
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
19 days ago • updated 18 days ago
Henry
▴ 10
0
votes
4
replies
216
views
Storing directories inside an ExperimentHub package?
ExperimentHub
20 days ago • updated 19 days ago
Tim Barry
• 0
0
votes
0
replies
92
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
19 days ago
communication
• 0
3
votes
6
replies
258
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
19 days ago
nhaus
▴ 30
0
votes
1
reply
165
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago
Shefali
• 0
0
votes
0
replies
120
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
20 days ago
Eryn
• 0
0
votes
0
replies
80
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
20 days ago
Dennis
• 0
0
votes
1
reply
147
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 16 days ago by
Guido Hooiveld
★ 3.9k • written 20 days ago by
Lucie
• 0
8
votes
23
replies
899
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 19 days ago by
Robert Castelo
★ 3.3k • written 20 days ago by
Bine
▴ 40
0
votes
1
reply
129
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Merav
• 0
0
votes
2
replies
206
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 21 days ago by
Michael Love
41k • written 25 days ago by
nhaus
▴ 30
0
votes
1
reply
152
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 21 days ago by
Michael Love
41k • written 21 days ago by
Adelaide
• 0
0
votes
2
replies
226
views
Regressing out batch effects
DESeq2
updated 21 days ago by
Michael Love
41k • written 26 days ago by
kys91240
• 0
5
votes
6
replies
411
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 17 days ago by
ATpoint
★ 4.1k • written 21 days ago by
nhaus
▴ 30
0
votes
1
reply
143
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
zh9118
• 0
1
vote
6
replies
473
views
GSVA on separate healthy and disease datasets
GSVA
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
Lucy
▴ 60
0
votes
0
replies
102
views
ggtree tip label position (depth)
ggtree
21 days ago • updated 20 days ago
Roope
• 0
2
votes
6
replies
375
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
22 days ago
Chris
• 0
0
votes
1
reply
171
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
BCS12
• 0
0
votes
0
replies
133
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
22 days ago
arne.sahm
• 0
0
votes
0
replies
90
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
22 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
431
views
Obtaining pheno data from CEL files
GEO
affy
28 days ago • updated 21 days ago
Kurtis
• 0
0
votes
1
reply
153
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 24 days ago by
Gordon Smyth
50k • written 25 days ago by
avery
• 0
1
vote
3
replies
238
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
215
views
MethylKit read issue
methylKit
updated 25 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 25 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
297
views
Help with design.matrix
limma
25 days ago • updated 24 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
136
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
25 days ago
andromeda
• 0
0
votes
2
replies
152
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
181
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 25 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
121
views
Granges regionCounts not returning the expected number of entries
methylKit
26 days ago • updated 25 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
93
views
flowDensity on a flowset
flowDensity
26 days ago
fredrikwallberg
• 0
1
vote
1
reply
157
views
DESeq2 - Missing values in count matrix
DESeq2
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 26 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
224
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 27 days ago by
Tim Peters
▴ 170 • written 27 days ago by
Kim
• 0
0
votes
0
replies
82
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
27 days ago
Macsue
• 0
1
vote
4
replies
422
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 26 days ago by
Gordon Smyth
50k • written 27 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 27 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
751
views
error in install immunedeconv
Install
updated 27 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
409
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 27 days ago by
Michael Love
41k • written 27 days ago by
RL
• 0
0
votes
2
replies
179
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
27 days ago
Gimena
• 0
0
votes
2
replies
152
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
27 days ago
Marianna
▴ 20
45,595 results • Page
3 of 912
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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