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
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 6 days ago
shepherl
3.8k
0
votes
1
reply
115
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 7 days ago by
James W. MacDonald
65k • written 10 days ago by
tian.liu0720
• 0
1
vote
2
replies
107
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
7 days ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
95
views
what is the sampleFiles
chipseq
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
zhulin
• 0
1
vote
1
reply
154
views
Differentially expressed genes in monocle pseudotime
monocle
updated 7 days ago by
Gordon Smyth
50k • written 9 days ago by
kthapa
• 0
4
votes
8
replies
331
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 5 days ago by
Peter Hickey
▴ 740 • written 12 days ago by
Juan Higareda
• 0
3
votes
3
replies
164
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
11 days ago • updated 5 days ago
jacques.imbert
• 0
0
votes
1
reply
120
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 7 days ago by
kamryncole1963
• 0 • written 12 days ago by
Sara
• 0
0
votes
3
replies
168
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 days ago
Virangika
• 0
0
votes
0
replies
56
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
8 days ago
Henry
▴ 10
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
0
votes
4
replies
225
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
1
vote
2
replies
314
views
GSVA error
GSVA
9 days ago • updated 8 days ago
Alex
• 0
2
votes
3
replies
289
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
8 days ago • updated 7 days ago
daniel.carbajo
• 0
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 15 days ago by
Netanel
• 0
1
vote
3
replies
317
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 8 days ago by
Gordon Smyth
50k • written 13 days ago by
Simran
• 0
0
votes
1
reply
108
views
Deseq2 Rlog transformation
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Sahar
• 0
0
votes
1
reply
678
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 11 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
11 days ago • updated 10 days ago
hemantcnaik
• 0
2
votes
2
replies
163
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
11 days ago
julia_mcdonough
• 0
2
votes
2
replies
143
views
[DiffBind] Obtaining normalization factors
DiffBind
11 days ago • updated 7 days ago
Henry
▴ 10
0
votes
1
reply
115
views
Bioinformatics student
Des
DESeq2
updated 11 days ago by
hemantcnaik
• 0 • written 11 days ago by
Sahar
• 0
0
votes
0
replies
69
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
11 days ago
shepherl
3.8k
2
votes
2
replies
144
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
11 days ago • updated 8 days ago
daniel.carbajo
• 0
0
votes
3
replies
218
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 days ago by
W. Evan Johnson
▴ 850 • written 11 days ago by
schlumbohm
• 0
5
votes
9
replies
844
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 5 days ago
Chris
• 0
0
votes
0
replies
73
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
11 days ago
Stevie Pederson
• 0
2
votes
2
replies
349
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
12 days ago • updated 11 days ago
Henry
▴ 10
0
votes
4
replies
196
views
Storing directories inside an ExperimentHub package?
ExperimentHub
13 days ago • updated 12 days ago
Tim Barry
• 0
0
votes
0
replies
78
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
12 days ago
communication
• 0
3
votes
6
replies
225
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
12 days ago
nhaus
▴ 30
0
votes
1
reply
152
views
DESeq2 gives an error and R crashes
DESeq2
13 days ago • updated 12 days ago
Shefali
• 0
0
votes
0
replies
109
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
13 days ago
Eryn
• 0
0
votes
0
replies
73
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
13 days ago
Dennis
• 0
0
votes
1
reply
127
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 9 days ago by
Guido Hooiveld
★ 3.9k • written 13 days ago by
Lucie
• 0
8
votes
23
replies
831
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 12 days ago by
Robert Castelo
★ 3.3k • written 13 days ago by
Bine
▴ 40
0
votes
1
reply
117
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 13 days ago by
ATpoint
★ 4.0k • written 15 days ago by
Merav
• 0
0
votes
2
replies
191
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 13 days ago by
Michael Love
41k • written 18 days ago by
nhaus
▴ 30
0
votes
1
reply
135
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
Adelaide
• 0
0
votes
2
replies
219
views
Regressing out batch effects
DESeq2
updated 14 days ago by
Michael Love
41k • written 19 days ago by
kys91240
• 0
5
votes
6
replies
391
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.0k • written 14 days ago by
nhaus
▴ 30
0
votes
1
reply
128
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
zh9118
• 0
1
vote
6
replies
447
views
GSVA on separate healthy and disease datasets
GSVA
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
Lucy
▴ 60
0
votes
0
replies
87
views
ggtree tip label position (depth)
ggtree
14 days ago • updated 13 days ago
Roope
• 0
2
votes
6
replies
336
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
15 days ago
Chris
• 0
0
votes
1
reply
158
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
BCS12
• 0
0
votes
0
replies
117
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
15 days ago
arne.sahm
• 0
0
votes
0
replies
81
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
15 days ago
Wolfgang Huber
★ 13k
45,567 results • Page
2 of 912
Recent ...
Replies
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
i.sudbery
▴ 40
Scholar
to
Michael Love
41k
Popular Question
to
shepherl
3.8k
Popular Question
to
taur.vil
• 0
Locations
• All
United Kingdom,
just now
France,
8 minutes ago
Melbourne, Australia,
45 minutes ago
United States,
1 hour ago
United States,
1 hour ago
Traffic: 582 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