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
840
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
2.7 years ago
barrypraveen
• 0
2
votes
2
replies
945
views
How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.7 years ago
f_rahmdani
• 0
1
vote
3
replies
1.3k
views
Recount3 data correspond to TCGA data
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.7 years ago by
kevin lee
• 0
0
votes
1
reply
2.5k
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Alessia
• 0
0
votes
0
replies
995
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.7 years ago
Levi
• 0
0
votes
3
replies
1.4k
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
alan.g.hudson
• 0
1
vote
3
replies
2.5k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 2.7 years ago by
Guido Hooiveld
★ 4.1k • written 2.7 years ago by
m-bihie
▴ 10
0
votes
0
replies
408
views
How to set dropout rate using splatSimDropout function of splatter ?
lazappi
2.7 years ago
shamsuzzaman86
• 0
0
votes
0
replies
776
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
2.7 years ago
Luca
• 0
0
votes
0
replies
1.1k
views
Confusing DSS outputs with smoothing (DMLtest)
DSS
2.8 years ago
Weisheng
• 0
0
votes
3
replies
1.3k
views
DRIMseq error for paired sample analysis
DRIMSeq
2.8 years ago • updated 2.7 years ago
Luca
• 0
0
votes
1
reply
927
views
Error in names(label_color[label_color == "organe"]) <- "lysosome" : 'names' attribute [1] must be the same length as the vector [0]
EnhancedVolcano
updated 2.7 years ago by
elefth.pavlos
▴ 40 • written 2.8 years ago by
Phương Thùy
• 0
0
votes
0
replies
1.2k
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb
AnnotationDbi
Annotation
2.8 years ago • updated 2.7 years ago
ahiser
• 0
0
votes
2
replies
1.7k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
2.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
611
views
Best practice for comparing a subset of data /
DESeq2
2.8 years ago
TzuChiao
▴ 10
0
votes
3
replies
1.4k
views
Annotated dendogram (tree) from tbl_graph
dendogram
ggtreeExtra
ggtree
annotation
Annotation
2.8 years ago
christian.dina
• 0
0
votes
0
replies
998
views
Using a clustree object to draw a "classical" dendogram
ggplot
dendogram
ggtreeExtra
clustree
ggtree
2.8 years ago
christian.dina
• 0
0
votes
1
reply
799
views
HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb )?
HiCDCPlus
updated 2.6 years ago by
merve.sahn
• 0 • written 2.8 years ago by
mlin18
• 0
0
votes
1
reply
792
views
How to adjust plots generated using psygenet2r?
psygenet2r
updated 2.8 years ago by
helucro
▴ 70 • written 2.8 years ago by
marinaw
▴ 20
0
votes
2
replies
1.1k
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 2.8 years ago by
pmadrigal
• 0 • written 2.8 years ago by
Kritikaverma2707
• 0
0
votes
0
replies
850
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.8 years ago
Giulia
• 0
1
vote
1
reply
1.0k
views
FlowSOM with unrelated channels
FlowSOM
cytofWorkflow
updated 2.8 years ago by
helucro
▴ 70 • written 2.8 years ago by
Anirban
• 0
0
votes
0
replies
819
views
Module Trait Corelation
WGCNA
2.8 years ago
allanokwaro
• 0
0
votes
1
reply
1.5k
views
Specific versions of packages
Bioconductor
updated 2.8 years ago by
Mike Smith
★ 6.6k • written 2.8 years ago by
Gábor Csárdi
▴ 90
0
votes
0
replies
757
views
getGEO error when trying to download a series matrix file
getGEOerror
2.8 years ago
suyonj
• 0
0
votes
0
replies
658
views
Align to reference genome
Alignment
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Antonio
• 0
0
votes
1
reply
1000
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
fuqichen1
• 0
0
votes
0
replies
819
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
2.8 years ago
edward.esiribloom
• 0
2
votes
1
reply
5.6k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 2.8 years ago by
RMiller
▴ 20 • written 2.8 years ago by
kevin
• 0
0
votes
0
replies
1.1k
views
Human to mouse SNP conversion
liftOver
SNP
GWASTools
2.8 years ago
bonheur
• 0
0
votes
0
replies
686
views
goMeth
missMethyl
2.8 years ago
anmolanp
▴ 10
0
votes
0
replies
769
views
Limma: Models containing an intercept and interactions with continuous variables.
limma
edgeR
DifferentialExpression
2.8 years ago
Aashil
• 0
0
votes
0
replies
922
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
2.8 years ago
Jitendra
▴ 10
0
votes
0
replies
502
views
Determining a delta G for full metabolic pathway changes
deltaG
metabolicmapping
2.8 years ago
chelsea.st.germain
• 0
0
votes
0
replies
751
views
Some questions regarding using limma and interpretation
limma
2.8 years ago
Sep
• 0
0
votes
1
reply
629
views
How to save primers in a local file with openPrimeR
openPrimeR
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
Santiago Edilberto
• 0
0
votes
1
reply
2.1k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 2.8 years ago by
Guido Hooiveld
★ 4.1k • written 2.8 years ago by
GenoMexa
• 0
0
votes
0
replies
890
views
rDGIdb package: score of the results
rDGIdb
r
2.8 years ago
HELEN
• 0
0
votes
0
replies
761
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.8 years ago
Ben J
▴ 20
4
votes
2
replies
1.2k
views
A way to find which genome builds a package supports
build
genome
2.8 years ago
Dmitry
• 0
1
vote
9
replies
3.9k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0
conumee
updated 13 months ago by
fraober
• 0 • written 2.8 years ago by
luca.s
▴ 50
0
votes
0
replies
749
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
2.8 years ago
zhiyi
• 0
2
votes
1
reply
1.5k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 2.4 years ago by
wrab425
• 0 • written 2.8 years ago by
snijesh
▴ 200
0
votes
0
replies
546
views
DMRcaller Neighborhood method
DMRcaller
2.8 years ago
Sarah
• 0
5
votes
2
replies
2.6k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 5 months ago by
hicks
• 0 • written 2.8 years ago by
jenniewoo
▴ 80
0
votes
1
reply
851
views
Definition of disease_subtype abbreviations
curatedMetagenomicData
updated 2.8 years ago by
Lucas Schiffer
▴ 240 • written 2.8 years ago by
Sehyun Oh
▴ 10
0
votes
0
replies
1.3k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
2.8 years ago
Manav
• 0
0
votes
0
replies
1.1k
views
Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools
ChIPseeker
2.8 years ago
840842906
• 0
0
votes
0
replies
588
views
Single Series Time Course
tissueTreg
2.8 years ago
guang-hui
• 0
0
votes
0
replies
900
views
data truncation with sce2fcs()
CATALYST
2.8 years ago
Shaun
• 0
1,000 results • Page
13 of 20
Recent ...
Replies
Answer: Guitar R package requires update due to dependency GenomicFeatures
by
Kevin Blighe
★ 4.0k
Greetings, This issue is indeed caused by recent changes in the Bioconductor 3.20+ release cycle. The function makeTxDbFromGFF() was previ…
Answer: ATACseq rudimentary questions
by
Kevin Blighe
★ 4.0k
For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
Answer: Clarification on counting in Rsubread (featureCounts)
by
Kevin Blighe
★ 4.0k
Dear Luca, This is a very plausible behavior caused by **read assignment ambiguity** due to **overlapping gene coordinates** (specifical…
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
by
Gordon Smyth
53k
The warning message is telling you that you already have the packages installed. However, you might consider upgrading to the current vers…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
Frank
• 0
Created by French developer Julien "Orteil" Thiennot, Cookie Clicker transformed the gaming landscape by introducing a new genre of idle ga…
Votes
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
Answer: Limma-voom sample weights and impact on DEG numbers
Awards
• All
Teacher
to
Gordon Smyth
53k
Popular Question
to
shepherl
4.2k
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Istvan Albert
▴ 50
Locations
• All
The Netherlands,
18 minutes ago
United States,
18 minutes ago
United States,
35 minutes ago
The Cave, 181 Longwood Avenue, Boston, USA,
54 minutes ago
WEHI, Melbourne, Australia,
2 hours ago
Traffic: 2451 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