7
votes
6
replies
646
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 16 days ago by • 0
8
votes
41
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 54 minutes ago by • 0 • written 5.5 years ago by ★ 4.0k
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
4
votes
5
replies
344
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 6 days ago Chris ▴ 10
0
votes
4
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 4 days ago by • 0 • written 19 months ago by ▴ 70
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 4 days ago by • 0 • written 7.9 years ago by • 0
1
vote
2
replies
106
views
Subsetting RNAseq data | voomaByGroup()
limma
3 days ago • updated 1 day ago Anna • 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 6 days ago by • 0 • written 5.2 years ago by ▴ 50
0
votes
4
replies
159
views
error running enricher from clusterprofiler
clusterProfiler cluster
6 days ago Yael • 0
0
votes
2
replies
756
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 6 days ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
156
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 days ago by 50k • written 6 days ago by • 0
2
votes
4
replies
193
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
1
vote
2
replies
210
views
Citation for edgeR user guide
edgeR
written 28 days ago by ▴ 30
1
vote
2
replies
123
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 days ago Patadù ▴ 10
0
votes
3
replies
141
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 7 days ago by • 0
2
votes
1
reply
92
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 6 days ago by ★ 1.9k • written 8 days ago by • 0
0
votes
2
replies
959
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 6 days ago by • 0 • written 18 months ago by • 0
1
vote
2
replies
149
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
7 days ago • updated 6 days ago Daniel • 0
2
votes
3
replies
153
views
Problem installing ChAMP on a MacBook
ChAMP
updated 5 days ago by 3.9k • written 5 days ago by • 0
4
votes
9
replies
293
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
2
votes
2
replies
415
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
9 days ago • updated 5 days ago Matthew Thornton ▴ 360
0
votes
2
replies
133
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
5 days ago makala • 0
2
votes
5
replies
244
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
6 days ago • updated 4 days ago Patadù ▴ 10
0
votes
5
replies
158
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC batchinDeseq2. columnsincolData.
2 days ago • updated 1 day ago Galina • 0
1
vote
1
reply
68
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 1 day ago by 66k • written 1 day ago by • 0
1
vote
1
reply
168
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 1 day ago by 66k • written 1 day ago by • 0
0
votes
1
reply
68
views
ERROR; return code from pthread_create() is 22
affy
updated 1 day ago by 66k • written 3 days ago by • 0
0
votes
6
replies
563
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 1 day ago Ken C • 0
0
votes
2
replies
72
views
How to run allelic imbalance in apeglm
apeglm
updated 1 day ago by 42k • written 2 days ago by ▴ 20
1
vote
3
replies
265
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 days ago by 50k • written 8 days ago by • 0
1
vote
3
replies
113
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
0
votes
2
replies
68
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
written 1 day ago by ▴ 40
0
votes
1
reply
40
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
updated 9 hours ago by 66k • written 10 hours ago by ▴ 10
0
votes
1
reply
48
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 8 hours ago by 66k • written 23 hours ago by • 0
0
votes
1
reply
51
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix Bioconductor
6 hours ago minardsmitha ▴ 10
0
votes
1
reply
39
views
recount3 problem downloading data from source sra
recount3
updated 5 hours ago by ★ 1.0k • written 8 hours ago by • 0
0
votes
0
replies
58
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
5 days ago k200987 • 0
0
votes
0
replies
20
views
Job: Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting
1 day ago pierre.devillemereuil • 0
0
votes
1
reply
726
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 7 hours ago by • 0 • written 4.7 years ago by ▴ 80
0
votes
2
replies
228
views
Visium RNA
metaMSdata
written 9 weeks ago by • 0
0
votes
0
replies
64
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
5 days ago Shaimaa Gamal • 0
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.0 years ago by ▴ 30
0
votes
0
replies
19
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
9 hours ago • updated 7 hours ago Raghad • 0
0
votes
0
replies
63
views
determine k during RUVSeq
RUVSeq RUVnormalize
5 days ago Ειρήνη • 0
0
votes
0
replies
19
views
Conditional analysis
GENESIS
9 hours ago SuperDad • 0
0
votes
5
replies
262
views
ChAMP installation issue
Cha ChAMP
updated 8 hours ago by 3.9k • written 8 days ago by • 0
1
vote
2
replies
263
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 5 days ago BioinfGuru ▴ 30
0
votes
0
replies
15
views
Spam: Unveiling Unmatched Best Custom Patches
SIMAT
5 days ago oliverelijhan 0
0
votes
0
replies
49
views
Difference in Contrast in DiffBind
DiffBind
6 days ago zzrammal • 0
0
votes
0
replies
93
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
5 days ago Anton01 • 0
58 results • Page 1 of 2
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
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…
Votes
Comment: Ensembl plants at annotationHub?
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
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
United States, 2 minutes ago
United States, 45 minutes ago
United States, 58 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 468 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