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
0
replies
11
views
News:
Legacy Bioconductor Installation
Installation
Bioconductor
5 hours ago
shepherl
3.9k
0
votes
1
reply
31
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 5 hours ago by
Robert Castelo
★ 3.3k • written 7 hours ago by
michelafrancesconi8
• 0
0
votes
4
replies
60
views
Cannot install oligo on Fedora
oligo
source
Install
updated 2 hours ago by
James W. MacDonald
66k • written 7 hours ago by
Guido Hooiveld
★ 4.0k
0
votes
1
reply
38
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
updated 11 hours ago by
ATpoint
★ 4.2k • written 12 hours ago by
sukeshinik5
• 0
0
votes
0
replies
12
views
News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
12 hours ago
info
▴ 10
0
votes
2
replies
49
views
Cluster columns in Pheatmap
geneexp
pheatmap
heatmaps
cluster
updated 9 hours ago by
James W. MacDonald
66k • written 12 hours ago by
pehove2385
• 0
0
votes
3
replies
90
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
1 day ago • updated 1 hour ago
tjl
• 0
0
votes
1
reply
39
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 8 hours ago by
James W. MacDonald
66k • written 1 day ago by
adendekk
• 0
0
votes
0
replies
24
views
News:
Bioconductor Build System
Builds
Bioconductor
1 day ago
shepherl
3.9k
0
votes
0
replies
27
views
News:
BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23
BioC2024
Conference
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
4
replies
222
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 15 hours ago by
Wei Shi
★ 3.6k • written 1 day ago by
atan
• 0
0
votes
0
replies
18
views
Job:
Bioinformatics MSc University of York
bioinformatics
JobPosting
1 day ago
Daphne
• 0
2
votes
2
replies
89
views
unable to access bioconductor packages - qvalue installation failed...
Install
updated 1 day ago by
shepherl
3.9k • written 1 day ago by
gabry.scata
▴ 10
5
votes
6
replies
294
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 1 day ago by
merv
▴ 120 • written 1 day ago by
Lorena Pantano
▴ 140
2
votes
2
replies
71
views
Get gene symbols for a set of hg19 coordinates
annotation
hg19
2 days ago • updated 1 day ago
pcantalupo
▴ 10
2
votes
4
replies
143
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install
GenomeInfoDbData
GenomeInfoDb
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
Brandon
▴ 20
1
vote
8
replies
147
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
2 days ago
boczniak767
▴ 720
0
votes
0
replies
30
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
2 days ago • updated 1 day ago
abhisek001
• 0
0
votes
3
replies
106
views
pathview error
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Fara
• 0
0
votes
5
replies
258
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 1 day ago by
xuz
• 0 • written 3 days ago by
minardsmitha
▴ 10
4
votes
3
replies
148
views
recount3 problem downloading data from source sra
recount3
updated 2 days ago by
Leonardo Collado Torres
★ 1.1k • written 3 days ago by
PABLO ANTONIO
▴ 10
0
votes
0
replies
36
views
Conditional analysis
GENESIS
3 days ago
SuperDad
• 0
0
votes
0
replies
37
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
3 days ago
Raghad
• 0
2
votes
2
replies
122
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
3 days ago • updated 2 days ago
mohammedtoufiq91
▴ 10
1
vote
1
reply
81
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 3 days ago by
James W. MacDonald
66k • written 3 days ago by
Tim Barry
• 0
0
votes
2
replies
107
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
4 days ago • updated 1 day ago
landenshanie
▴ 40
0
votes
0
replies
31
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
4 days ago
pierre.devillemereuil
• 0
1
vote
1
reply
88
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
Đình Vinh
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
4 days ago
shahrozimmac
0
1
vote
1
reply
188
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
ttt
• 0
0
votes
0
replies
40
views
Processing of curatedmetagenomics
curatedMetagenomicData
4 days ago
Edward
• 0
1
vote
3
replies
145
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 4 days ago by
James W. MacDonald
66k • written 5 days ago by
boczniak767
▴ 720
1
vote
2
replies
92
views
How to run allelic imbalance in apeglm
apeglm
updated 4 days ago by
Michael Love
42k • written 5 days ago by
euge.eugenio
▴ 20
0
votes
0
replies
46
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
5 days ago
Bibi
• 0
0
votes
5
replies
188
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
5 days ago • updated 4 days ago
Galina
• 0
1
vote
2
replies
125
views
Subsetting RNAseq data | voomaByGroup()
limma
6 days ago • updated 4 days ago
Anna
• 0
0
votes
1
reply
84
views
ERROR; return code from pthread_create() is 22
affy
updated 4 days ago by
James W. MacDonald
66k • written 6 days ago by
pickingastar
• 0
0
votes
0
replies
56
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
6 days ago • updated 5 days ago
Abiologist
• 0
2
votes
4
replies
220
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 4 days ago by
Michael Love
42k • written 7 days ago by
shaunpeterson
• 0
0
votes
3
replies
143
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 7 days ago by
damian.szk
▴ 80 • written 7 days ago by
ninidea
• 0
0
votes
6
replies
605
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
7 days ago • updated 4 days ago
Ken C
• 0
0
votes
2
replies
145
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
8 days ago
makala
• 0
0
votes
0
replies
73
views
determine k during RUVSeq
RUVSeq
RUVnormalize
8 days ago
Ειρήνη
• 0
0
votes
0
replies
74
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
8 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
8 days ago
oliverelijhan
0
0
votes
0
replies
96
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
8 days ago
Anton01
• 0
2
votes
3
replies
188
views
Problem installing ChAMP on a MacBook
ChAMP
updated 8 days ago by
shepherl
3.9k • written 8 days ago by
Galia
• 0
0
votes
0
replies
69
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
8 days ago
danalvoronov
▴ 10
0
votes
0
replies
65
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
8 days ago
k200987
• 0
2
votes
5
replies
268
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
9 days ago • updated 7 days ago
Patadù
▴ 10
181 results • Page
1 of 4
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function
by
Robert Castelo
★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Awards
• All
Popular Question
to
Robert Castelo
★ 3.3k
Popular Question
to
kevin.rue
▴ 350
Popular Question
to
Wei Shi
★ 3.6k
Popular Question
to
Gordon Smyth
50k
Popular Question
to
jovel_juan
▴ 30
Locations
• All
United States,
1 minute ago
UPF, Barcelona, Spain,
7 minutes ago
WEHI, Melbourne, Australia,
16 minutes ago
United States,
43 minutes ago
Belgium,
1 hour ago
Traffic: 351 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