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
0
votes
2
replies
156
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
18 days ago • updated 17 days ago
Seongsu
• 0
0
votes
1
reply
128
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 17 days ago by
James W. MacDonald
65k • written 19 days ago by
ja569116
• 0
0
votes
2
replies
157
views
Gene Ontology doubt
microbiomeExplorer
19 days ago • updated 15 days ago
Bhawna
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
19 days ago • updated 14 days ago
fer_talavera
• 0
1
vote
2
replies
191
views
MethylKit read issue
methylKit
updated 14 days ago by
James W. MacDonald
65k • written 19 days ago by
CHEN
• 0
0
votes
2
replies
215
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 10 hours ago
isaac.vock
• 0
0
votes
7
replies
321
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 days ago • updated 17 days ago
needNGS
• 0
0
votes
1
reply
148
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 18 days ago by
Michael Love
41k • written 21 days ago by
saadmurtazakhan
▴ 10
14
votes
20
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 3 hours ago
Chris
• 0
0
votes
2
replies
155
views
Minfi - estimatecellscount
min
minfi
21 days ago
clacarion
• 0
0
votes
0
replies
94
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 days ago
feather-W
• 0
0
votes
0
replies
91
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 days ago
Ankit
▴ 20
1
vote
5
replies
289
views
fgsea fork
fgsea
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
yimjohns
• 0
3
votes
5
replies
327
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 20 days ago by
Gordon Smyth
50k • written 22 days ago by
Fabian
• 0
0
votes
6
replies
304
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 21 days ago by
Gordon Smyth
50k • written 22 days ago by
Faisal
• 0
0
votes
1
reply
134
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Mikushi
• 0
0
votes
2
replies
205
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
22 days ago • updated 17 days ago
w.cookson
• 0
0
votes
0
replies
79
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
22 days ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
111
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Karen
• 0
2
votes
3
replies
314
views
PCA of different bacterial species
DESeq2
updated 23 days ago by
Michael Love
41k • written 24 days ago by
Laura
▴ 10
2
votes
8
replies
474
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
Amit
• 0
1
vote
2
replies
208
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
24 days ago
Mj.A.
• 0
0
votes
2
replies
182
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 24 days ago by
Michael Love
41k • written 24 days ago by
SG
• 0
2
votes
2
replies
190
views
From a DNAStringSet to a data.frame
Biostrings
24 days ago
ramiro.barrantes
▴ 10
5
votes
25
replies
788
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 15 days ago by
Gordon Smyth
50k • written 25 days ago by
Jitendra
▴ 10
0
votes
2
replies
152
views
bioconductor emailing list
Bioconductor
updated 25 days ago by
shepherl
3.8k • written 25 days ago by
1427972815
• 0
2
votes
3
replies
225
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 24 days ago by
Wei Shi
★ 3.6k • written 25 days ago by
thomas.heigl.ibk
• 0
3
votes
2
replies
190
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
25 days ago
Anita
▴ 10
0
votes
0
replies
99
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
25 days ago
gshweta95
• 0
2
votes
1
reply
209
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 25 days ago by
ATpoint
★ 4.0k • written 26 days ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
334
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 25 days ago by
alan.ocallaghan
▴ 160 • written 26 days ago by
Najla Abassi
• 0
7
votes
6
replies
412
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
Amit
• 0
0
votes
2
replies
308
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
28 days ago • updated 17 days ago
Gordon
• 0
2
votes
1
reply
177
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
enee
▴ 10
0
votes
0
replies
118
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
28 days ago
Maria Doyle
▴ 70
0
votes
0
replies
107
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
28 days ago
shepherl
3.8k
0
votes
1
reply
148
views
collapseReplicates dimension error
DESeq2
Dese
updated 24 days ago by
Michael Love
41k • written 28 days ago by
Léa
• 0
0
votes
0
replies
99
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
29 days ago
nromerov
• 0
1
vote
2
replies
198
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
29 days ago • updated 23 days ago
Chanderkant Chaudhary
• 0
0
votes
1
reply
206
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
scoops_streams_06
• 0
1
vote
3
replies
231
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 29 days ago by
Marcel Ramos
690 • written 29 days ago by
Astrid Deschênes
• 0
5
votes
3
replies
665
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jack S.
▴ 50
0
votes
2
replies
199
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 weeks ago • updated 29 days ago
kcarey
• 0
0
votes
0
replies
109
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
4 weeks ago
mayra.haedo
• 0
0
votes
0
replies
103
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
4 weeks ago
taylor.witte
• 0
0
votes
0
replies
121
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
4 weeks ago
erbrocato
• 0
1
vote
4
replies
252
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
4 weeks ago
samuel.channon
• 0
0
votes
2
replies
182
views
Visium RNA
metaMSdata
updated 4 weeks ago by
vvvc360work2
• 0 • written 4 weeks ago by
Karlison
• 0
1
vote
2
replies
244
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 4 weeks ago by
ATpoint
★ 4.0k • written 4 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
104
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
4 weeks ago
BID
• 0
45,551 results • Page
3 of 912
Recent ...
Replies
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards
• All
Popular Question
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Popular Question
to
BioinfGuru
▴ 30
Popular Question
to
Gordon Smyth
50k
Scholar
to
Peter Hickey
▴ 740
Locations
• All
WEHI, Melbourne, Australia,
14 minutes ago
UPF, Barcelona, Spain,
15 minutes ago
France,
20 minutes ago
Heidelberg,
37 minutes ago
United States,
45 minutes ago
Traffic: 544 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