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1
vote
4
replies
362
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago
winwater0928
• 0
2
votes
9
replies
430
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 26 days ago by
James W. MacDonald
66k • written 26 days ago by
Alexandre
• 0
2
votes
5
replies
264
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 26 days ago by
James W. MacDonald
66k • written 27 days ago by
bandconductor
• 0
1
vote
2
replies
178
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
27 days ago • updated 26 days ago
ATpoint
★ 4.1k
0
votes
2
replies
269
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
28 days ago • updated 26 days ago
shuwangxinze1996
• 0
0
votes
8
replies
402
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 26 days ago by
swbarnes2
★ 1.4k • written 28 days ago by
Aaliya
• 0
0
votes
1
reply
168
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 27 days ago by
Michael Love
42k • written 27 days ago by
kcarey
• 0
2
votes
13
replies
501
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 weeks ago • updated 27 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
319
views
get BM error
ensembldb
updated 27 days ago by
James W. MacDonald
66k • written 27 days ago by
Fara
• 0
0
votes
5
replies
327
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 27 days ago by
James W. MacDonald
66k • written 4 weeks ago by
Gayatri
• 0
0
votes
0
replies
98
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
27 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
240
views
Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by
Michael Love
42k • written 27 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
896
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 27 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 27 days ago by
Basti
▴ 780 • written 29 days ago by
clacarion
• 0
3
votes
1
reply
330
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by
Michael Love
42k • written 28 days ago by
i.sudbery
▴ 40
0
votes
7
replies
760
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 28 days ago
shepherl
3.9k
1
vote
1
reply
137
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
87
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
28 days ago
info
▴ 10
3
votes
3
replies
255
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by
Michael Love
42k • written 29 days ago by
WardDeb
• 0
0
votes
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 28 days ago
hortense96
• 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 28 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 28 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
2
votes
4
replies
293
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
Mirella Aurora
• 0
4
votes
6
replies
479
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago
Jonathan
▴ 10
0
votes
1
reply
141
views
FDR via q-value
qvalue
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
John
• 0
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 29 days ago
shepherl
3.9k
3
votes
2
replies
241
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 29 days ago by
Guido Hooiveld
★ 4.0k • written 4 weeks ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
246
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 weeks ago • updated 29 days ago
catv
• 0
0
votes
0
replies
100
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
4 weeks ago
vaxahey107
• 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
109
views
I am trying to detect alternative splicing.
ASpli
4 weeks ago
Sebashish
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.4 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
822
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
272
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago
lonn
• 0
1
vote
2
replies
268
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
1
vote
0
replies
366
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 weeks ago
BioinfGuru
▴ 30
0
votes
7
replies
455
views
DESeq filtering specific to contrasts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
2
replies
285
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
7 weeks ago • updated 4 weeks ago
isaac.vock
• 0
1
vote
3
replies
198
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 weeks ago by
James W. MacDonald
66k • written 4 weeks ago by
bas_work
▴ 30
2
votes
5
replies
797
views
DESeq2 setting significant p-value
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
233
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 weeks ago by
James W. MacDonald
66k • written 4 weeks ago by
sansan
• 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
294
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
6
votes
5
replies
483
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 11 weeks ago by
Kim
• 0
0
votes
3
replies
219
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
0
votes
2
replies
153
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
2
replies
930
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 4 weeks ago by
Garrett
• 0 • written 9.2 years ago by
brohawndg
▴ 150
0
votes
4
replies
233
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
1,000 results • Page
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Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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