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
8
replies
2.2k
views
translate errors in fastq file reading
translate
biostrings
Biostrings
3.2 years ago
Brett
• 0
0
votes
3
replies
2.6k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2
Toil
RSEM
3.2 years ago
Niveditha
▴ 20
1
vote
4
replies
3.3k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2
plotCounts
vst
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Laia
▴ 10
4
votes
5
replies
2.8k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 2.2 years ago by
jacorvar
▴ 40 • written 3.2 years ago by
eraldagjika
▴ 20
2
votes
13
replies
4.2k
views
Too much data for Diffbind
DiffBind
updated 14 months ago by
Ou, Jianhong
★ 1.3k • written 3.2 years ago by
littlefishes20
▴ 10
0
votes
4
replies
1.4k
views
Error installing Bioc
clusterProfiler
Bioconductor
BiocManager
updated 3.2 years ago by
Guido Hooiveld
★ 4.1k • written 3.2 years ago by
Javier
• 0
0
votes
3
replies
4.7k
views
Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 2.4 years ago by
olatunbosun.arowolo
• 0 • written 3.2 years ago by
shuangshuang
• 0
1
vote
4
replies
1.6k
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA
gene
RNASeqRData
edgeR
geneontology
3.2 years ago
faiza
• 0
1
vote
1
reply
1.3k
views
creating a NOT gate for gating out a single quadrant in a quadrant gate openCyto
FlowCytometry
Opencyto
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 3.2 years ago by
Noël
• 0
3
votes
12
replies
3.6k
views
Replicates in DESeq2
DESeq2
updated 3.2 years ago by
Yijing
• 0 • written 4.4 years ago by
leo.dagata
▴ 10
1
vote
2
replies
1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
Flavio
• 0
1
vote
2
replies
1.0k
views
A quick question on “Biostrings” package
local
Smith-Watermanmatrix;
Biostrings;
3.2 years ago • updated 3.1 years ago
happymonan
• 0
1
vote
3
replies
1.2k
views
What should I do with RNA-Seq data to get a gene that work?
find
RNASeqRData
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
yuhang
• 0
0
votes
4
replies
1.1k
views
DESeq2 design with continuous variables AND filtering of low counts
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
bgurdon
• 0
0
votes
0
replies
867
views
gate_quad_sequential as parent gate for downstream gating in opencyto CSV template
opencyto
FlowCytometry
3.2 years ago
Noël
• 0
3
votes
1
reply
1.1k
views
Should I set a seed prior to running AUCell?
AUCell
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
Lucy
▴ 60
0
votes
2
replies
1.3k
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
3.2 years ago
Monica
• 0
1
vote
11
replies
3.1k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Hasher
• 0
2
votes
8
replies
2.0k
views
Errors when plotting data using heatmap_GO (GOexpress)
GOexpress
updated 3.2 years ago by
kevin.rue
▴ 350 • written 3.2 years ago by
grolo
• 0
2
votes
4
replies
1.7k
views
DiffBind and peak counts as input
DESeq2
edgeR
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.2 years ago by
Bogdan
▴ 670
2
votes
6
replies
12k
views
Unable to download packages from Bioconductor
downloading-issue
updated 3.2 years ago by
W
• 0 • written 3.5 years ago by
Aryan
▴ 10
2
votes
2
replies
1.1k
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
3.2 years ago
evan.j.williams
▴ 10
3
votes
12
replies
3.8k
views
t.test to determine the P-value in DESeq2
DESeq2
written 3.2 years ago by
Maryam.sed1400
• 0
2
votes
4
replies
1.9k
views
Advice on ANCOMBC 'R CMD build' error for BioC 3.16
BuildReport
updated 3.2 years ago by
shepherl
4.2k • written 3.2 years ago by
HULFRED
▴ 10
2
votes
3
replies
2.7k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
updated 8 months ago by
ben
• 0 • written 3.2 years ago by
L
▴ 50
2
votes
2
replies
3.0k
views
Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed while using DESeq2
DESeq2
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
keremozdel9
• 0
4
votes
2
replies
5.4k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
3.2 years ago
Wuschel
▴ 10
0
votes
17
replies
4.3k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 2.9 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Sam
• 0
0
votes
2
replies
2.4k
views
Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2
Install
r
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
Catherine
• 0
0
votes
8
replies
1.7k
views
disappearing of DEGs genes by adjusting P-value < 0.05
DESeq2
3.2 years ago
Maryam.sed1400
• 0
0
votes
4
replies
3.2k
views
How to sort SAM file
samtool
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.3 years ago by
Maryam.sed1400
• 0
0
votes
2
replies
1.3k
views
News:
List of Deprecated Packages for Bioc3.16
Release
Deprecation
Devel
Bioconductor
3.2 years ago
shepherl
4.2k
2
votes
2
replies
1.1k
views
Second covariate
DESeq2
3.2 years ago
liberios
▴ 10
0
votes
2
replies
1.7k
views
Unable to over/ride colour scheme with custom key-value pairs
EnhancedVolcano
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 3.2 years ago by
patrirodry85
• 0
1
vote
7
replies
1.8k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2
edgeR
updated 3.1 years ago by
chaco001
• 0 • written 3.2 years ago by
Bogdan
▴ 670
0
votes
5
replies
1.8k
views
Inquiry about suitable package for proteomics study design
Proteomics
design
updated 3.2 years ago by
evocanres
• 0 • written 3.2 years ago by
proteome_AO
• 0
0
votes
1
reply
1.1k
views
DESeq2 - Differential expression for miRNA data
DESeq2
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
Mariane
• 0
1
vote
1
reply
938
views
News:
Bioconductor Hacktoberfest meetups!
meetup
hacktoberfest
3.2 years ago
Maria Doyle
▴ 110
0
votes
0
replies
906
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.2 years ago
nattzy94
▴ 20
0
votes
4
replies
3.0k
views
how do i read a .seq file?
Bioconductor
3.2 years ago
Luis
• 0
0
votes
2
replies
1.1k
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
3.2 years ago
Yijing
• 0
0
votes
2
replies
1.2k
views
Shivani
kegg
updated 3.2 years ago by
deeenes
▴ 60 • written 3.2 years ago by
Shivani
• 0
2
votes
2
replies
1.3k
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
3.2 years ago
dario.beraldi
• 0
3
votes
9
replies
2.3k
views
scDblFinder and xgboost
scDblFinder
xgboost
written 3.7 years ago by
Bogdan
▴ 670
3
votes
3
replies
1.8k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
3.2 years ago
duhwa.lee
• 0
0
votes
3
replies
1.6k
views
Issue with module-trait analysis in BioNero
BioNERO
updated 3.2 years ago by
Fabricio Almeida-Silva
▴ 40 • written 3.2 years ago by
Biologist
• 0
0
votes
4
replies
1.9k
views
Skew of differentially expressed genes using DESeq2
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
b88dfe53
• 0
4
votes
4
replies
6.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 3.2 years ago by
12133067
• 0 • written 9.3 years ago by
enricoferrero
▴ 680
0
votes
2
replies
1.2k
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
3.2 years ago
michela
▴ 20
0
votes
0
replies
1.0k
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
3.2 years ago
rridley3
• 0
46,706 results • Page
73 of 935
Recent ...
Replies
Comment: How to do differential expresion across time serise with edgeR?
by
petergrahamclark
▴ 10
The use case is kinetic model parameterisation. I'm actually a systems biologist not a bioinformatician. (which is why I'm struggling here)…
Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaasocissalpc
• 0
Just like attending workshops helps you improve skills in a field, playing 8 Ball Pool helps sharpen your strategy and precision. You can d…
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
TikTsokaasocissalpc
• 0
Thanks for sharing this update. Clear migration timelines and documentation are essential for learners and researchers alike. In healthcare…
Comment: ATACseq rudimentary questions
by
4747
• 0
Thank you so much for being detailed, all makes sense now
Answer: How to do differential expresion across time serise with edgeR?
by
Gordon Smyth
53k
You actually haven't done any DE analysis at all, you've just selected for genes with either zero or large D0 counts. Another issue is tha…
Votes
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
A: limma-voom duplicateCorrelation once or twice, difference?
A: limma: comparison of repeat measurements - blocking or within-subject correlatio
Answer: DecideTest vs topTAGs in edgeR
A: LIMMA time series spline model.matrix design setup
Awards
• All
Popular Question
to
Gordon Smyth
53k
Popular Question
to
ZheFrench
▴ 60
Popular Question
to
shepherl
4.2k
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Locations
• All
United States,
59 minutes ago
United States,
1 hour ago
Barcelona, Spain,
3 hours ago
United States,
3 hours ago
United Kingdom,
4 hours ago
Traffic: 660 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