Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
1
vote
2
replies
474
views
GSVA error
GSVA
17 days ago • updated 16 days ago
Alex
• 0
2
votes
3
replies
315
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago
daniel.carbajo
• 0
3
votes
3
replies
313
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 23 days ago by
Netanel
• 0
1
vote
3
replies
340
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
1
reply
125
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
0
votes
1
reply
695
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 19 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
187
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago • updated 18 days ago
hemantcnaik
• 0
2
votes
2
replies
186
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
19 days ago
julia_mcdonough
• 0
2
votes
2
replies
165
views
[DiffBind] Obtaining normalization factors
DiffBind
19 days ago • updated 15 days ago
Henry
▴ 10
0
votes
1
reply
129
views
Bioinformatics student
Des
DESeq2
updated 19 days ago by
hemantcnaik
• 0 • written 19 days ago by
Sahar
• 0
0
votes
0
replies
81
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
19 days ago
shepherl
3.8k
2
votes
2
replies
166
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
19 days ago • updated 17 days ago
daniel.carbajo
• 0
0
votes
3
replies
248
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 13 days ago by
W. Evan Johnson
▴ 850 • written 19 days ago by
schlumbohm
• 0
5
votes
9
replies
896
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 13 days ago
Chris
• 0
0
votes
0
replies
88
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
19 days ago
Stevie Pederson
• 0
2
votes
2
replies
377
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 days ago • updated 19 days ago
Henry
▴ 10
0
votes
4
replies
218
views
Storing directories inside an ExperimentHub package?
ExperimentHub
21 days ago • updated 20 days ago
Tim Barry
• 0
0
votes
0
replies
96
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
20 days ago
communication
• 0
3
votes
6
replies
263
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
20 days ago
nhaus
▴ 30
0
votes
1
reply
172
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago
Shefali
• 0
0
votes
0
replies
126
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 days ago
Eryn
• 0
0
votes
0
replies
84
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
21 days ago
Dennis
• 0
0
votes
1
reply
153
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 17 days ago by
Guido Hooiveld
★ 3.9k • written 21 days ago by
Lucie
• 0
8
votes
23
replies
908
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 20 days ago by
Robert Castelo
★ 3.3k • written 21 days ago by
Bine
▴ 40
0
votes
1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Merav
• 0
0
votes
2
replies
213
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
156
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
0
votes
2
replies
232
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
5
votes
6
replies
413
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 18 days ago by
ATpoint
★ 4.1k • written 22 days ago by
nhaus
▴ 30
0
votes
1
reply
146
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zh9118
• 0
1
vote
6
replies
475
views
GSVA on separate healthy and disease datasets
GSVA
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
Lucy
▴ 60
0
votes
0
replies
105
views
ggtree tip label position (depth)
ggtree
22 days ago • updated 21 days ago
Roope
• 0
2
votes
6
replies
382
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
23 days ago
Chris
• 0
0
votes
1
reply
175
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
BCS12
• 0
0
votes
0
replies
139
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
23 days ago
arne.sahm
• 0
0
votes
0
replies
94
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
23 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
437
views
Obtaining pheno data from CEL files
GEO
affy
29 days ago • updated 22 days ago
Kurtis
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 25 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
1
vote
3
replies
239
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
222
views
MethylKit read issue
methylKit
updated 26 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 26 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
301
views
Help with design.matrix
limma
26 days ago • updated 25 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
140
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
26 days ago
andromeda
• 0
0
votes
2
replies
156
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
183
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 26 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
126
views
Granges regionCounts not returning the expected number of entries
methylKit
27 days ago • updated 26 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
98
views
flowDensity on a flowset
flowDensity
27 days ago
fredrikwallberg
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 27 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
230
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 28 days ago by
Kim
• 0
204 results • Page
3 of 5
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards
• All
Scholar
to
Rory Stark
★ 5.2k
Popular Question
to
tangming2005
▴ 190
Popular Question
to
Ian D.
▴ 70
Popular Question
to
junhui.li11
• 0
Scholar
to
James W. MacDonald
65k
Locations
• All
WEHI, Melbourne, Australia,
just now
EMBL Heidelberg,
3 minutes ago
India,
8 minutes ago
United Kingdom,
44 minutes ago
Germany,
1 hour ago
Traffic: 591 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6