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votes
0
replies
10
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
8 hours ago
Melisa Tecik
• 0
0
votes
1
reply
52
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 17 hours ago by
ATpoint
★ 4.5k • written 17 hours ago by
siobhan.dietz
• 0
0
votes
1
reply
77
views
eRNAs count
RNASeq
DESeq2
updated 4 days ago by
ATpoint
★ 4.5k • written 4 days ago by
Irene
• 0
0
votes
0
replies
88
views
WGCNA module preservation using only adjacency matrix
WGCNA
9 days ago
yang1641
• 0
0
votes
0
replies
43
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
9 days ago
Simone
• 0
0
votes
2
replies
261
views
installation error for BiocNeighbors package
BiocNeighbors
9 days ago
育
• 0
0
votes
0
replies
86
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
11 days ago
elgomez
• 0
0
votes
1
reply
173
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
14 days ago • updated 8 days ago
abadgerw
• 0
0
votes
1
reply
281
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
14 days ago • updated 8 days ago
abadgerw
• 0
0
votes
0
replies
116
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
17 days ago
user_bioinfo
• 0
0
votes
0
replies
113
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
18 days ago
kim
• 0
0
votes
0
replies
102
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
18 days ago
daccar98
• 0
0
votes
0
replies
124
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
18 days ago
brayas13
• 0
0
votes
0
replies
102
views
export processed data from flowploidy
flowPloidy
22 days ago
Zdenek Skala
• 0
0
votes
0
replies
67
views
Filtering Steps for proActiv Analysis
Transcriptomics
proActiv
25 days ago • updated 24 days ago
LuciaNhu
• 0
0
votes
0
replies
97
views
diffbind covariates
DiffBind
ATACSeq
updated 26 days ago by
Michael Love
42k • written 27 days ago by
Alpesh Querer
▴ 220
0
votes
0
replies
74
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
27 days ago
mario_de_manner
• 0
0
votes
0
replies
77
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment
SingleCellExperiment
4 weeks ago
Ibrahim
• 0
0
votes
0
replies
86
views
DiffBind subset replicates
DiffBind
5 weeks ago
Haiping
• 0
0
votes
0
replies
112
views
Rsubread - sublong function
pacbio
sublong
Rsubread
5 weeks ago
thomas.heigl.ibk
• 0
0
votes
0
replies
108
views
when FOLD>0, which group of sampls increased?
BASiCS
6 weeks ago
Jeffcgen2000
• 0
0
votes
0
replies
117
views
Paired splsda
mixOmics
6 weeks ago
michelafrancesconi8
• 0
0
votes
0
replies
135
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
6 weeks ago
Young Boqin
• 0
0
votes
0
replies
147
views
DMRcate pcutoff setting
EpicV2
DMRcate
6 weeks ago
kitzhu
• 0
0
votes
0
replies
145
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS
alternativesplicing
maser
R
6 weeks ago
Anke
• 0
1
vote
1
reply
279
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 6 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 6 weeks ago by
Nasim
• 0
0
votes
1
reply
183
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel
ChIPQC
written 6 weeks ago by
Young Boqin
• 0
2
votes
6
replies
847
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
8 months ago • updated 6 weeks ago
María Calvo
• 0
0
votes
0
replies
144
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
7 weeks ago
Marco
• 0
1
vote
1
reply
228
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 7 weeks ago by
ATpoint
★ 4.5k • written 7 weeks ago by
Pimpa
• 0
1
vote
1
reply
582
views
Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 7 weeks ago by
Vince Schulz
▴ 160 • written 7 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
210
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
8 weeks ago • updated 7 weeks ago
tim.meese
• 0
0
votes
1
reply
259
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 8 weeks ago by
Mike Smith
★ 6.6k • written 8 weeks ago by
Abiologist
• 0
0
votes
0
replies
165
views
Deprecated Gates- tailgate
openCyto
8 weeks ago
ztflaten
• 0
0
votes
0
replies
172
views
Getting error while running GenomicPlot
GenomicPlot
8 weeks ago
Lucky
• 0
0
votes
0
replies
181
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
8 weeks ago
Fernanda
• 0
0
votes
0
replies
152
views
package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx
PXDataset
RforProteomics
8 weeks ago
Jane_Huang
• 0
0
votes
0
replies
297
views
Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools
SpatialDecon
GeoMxWorkflows
9 weeks ago
Cinque
• 0
0
votes
0
replies
198
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
9 weeks ago
Alejandro
• 0
0
votes
0
replies
237
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel
scran
BiocParall
9 weeks ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
245
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
10 weeks ago
Ragnhild
• 0
0
votes
1
reply
507
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
updated 9 weeks ago by
Aidan
▴ 60 • written 10 weeks ago by
semra
• 0
0
votes
1
reply
259
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 10 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 10 weeks ago by
emilymily77
• 0
0
votes
5
replies
686
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 6 weeks ago by
Yang Liao
▴ 450 • written 10 weeks ago by
venusian.martin
• 0
0
votes
2
replies
386
views
concentration tables suitable as input for new packages?
Bioconductor
10 weeks ago
katja.danielzik
• 0
0
votes
1
reply
274
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 10 weeks ago by
James W. MacDonald
67k • written 10 weeks ago by
bioinformaticssrm2011
• 0
0
votes
5
replies
615
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 8 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 10 weeks ago by
semra
• 0
0
votes
1
reply
288
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 11 weeks ago by
Vincent J. Carey, Jr.
6.7k • written 11 weeks ago by
kmzhou4
• 0
0
votes
0
replies
301
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets
differential-abundance
11 weeks ago
샤니쿠마리
• 0
2
votes
2
replies
657
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
11 weeks ago
Assa Yeroslaviz
★ 1.5k
1,000 results • Page
1 of 20
Recent ...
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Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
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