0
votes
4
replies
205
views
ChAMP installation issue
Cha ChAMP
updated just now by • 0 • written 8 days ago by • 0
0
votes
0
replies
5
views
Conditional analysis
GENESIS
8 minutes ago SuperDad • 0
0
votes
1
reply
17
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
updated 31 minutes ago by 66k • written 1 hour ago by ▴ 10
0
votes
0
replies
5
views
FindOverlaps, makeVennDiagram and "others"
peaks ChIPpeakAnno ATAC ATACSeq
36 minutes ago Raghad • 0
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.0 years ago by ▴ 30
0
votes
2
replies
225
views
Visium RNA
metaMSdata
written 8 weeks ago by • 0
7
votes
40
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 5 hours ago by ★ 2.0k • written 5.5 years ago by ★ 4.0k
0
votes
2
replies
58
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
written 18 hours ago by ▴ 40
0
votes
0
replies
22
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
14 hours ago Tim Barry • 0
0
votes
2
replies
740
views
Help with ENmix readidat
ENmix IlluminaHumanMethylationEPICmanifest
updated 18 hours ago by 66k • written 2.0 years ago by • 0
1
vote
3
replies
104
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 18 hours ago by 66k • written 1 day ago by ▴ 720
2
votes
4
replies
185
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 21 hours ago by 42k • written 3 days ago by • 0
0
votes
2
replies
69
views
How to run allelic imbalance in apeglm
apeglm
updated 21 hours ago by 42k • written 1 day ago by ▴ 20
0
votes
6
replies
558
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 22 hours ago Ken C • 0
0
votes
1
reply
64
views
ERROR; return code from pthread_create() is 22
affy
updated 23 hours ago by 66k • written 3 days ago by • 0
1
vote
1
reply
146
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 23 hours ago by 66k • written 1 day ago by • 0
1
vote
1
reply
56
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 23 hours ago by 66k • written 1 day ago by • 0
0
votes
0
replies
17
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
1
vote
2
replies
97
views
Subsetting RNAseq data | voomaByGroup()
limma
3 days ago • updated 1 day ago Anna • 0
0
votes
5
replies
153
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
0
votes
1
reply
41
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl microRNA starBase webapi ENCORI
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
0
votes
0
replies
12
views
Spam: Understanding Laser Hair Removal?
healthyControlsPresenceChecker
1 day ago shahrozimmac 0
7
votes
6
replies
642
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by • 0
0
votes
0
replies
25
views
Processing of curatedmetagenomics
curatedMetagenomicData
1 day ago Edward • 0
0
votes
0
replies
34
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
2 days ago Bibi • 0
0
votes
0
replies
48
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
3 days ago • updated 2 days ago Abiologist • 0
0
votes
3
replies
118
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 3 days ago by ▴ 80 • written 4 days ago by • 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 3 days ago by • 0 • written 7.9 years ago by • 0
2
votes
5
replies
231
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
5 days ago • updated 4 days ago Patadù ▴ 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
1
vote
2
replies
259
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 days ago • updated 4 days ago BioinfGuru ▴ 30
0
votes
2
replies
126
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
4 days ago makala • 0
2
votes
2
replies
409
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 4 days ago Matthew Thornton ▴ 360
0
votes
0
replies
60
views
determine k during RUVSeq
RUVSeq RUVnormalize
5 days ago Ειρήνη • 0
4
votes
9
replies
287
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
3
replies
139
views
Problem installing ChAMP on a MacBook
ChAMP
updated 5 days ago by 3.9k • written 5 days ago by • 0
0
votes
0
replies
62
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
5 days ago Shaimaa Gamal • 0
0
votes
0
replies
15
views
Spam: Unveiling Unmatched Best Custom Patches
SIMAT
5 days ago oliverelijhan 0
0
votes
0
replies
91
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
5 days ago Anton01 • 0
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
0
votes
0
replies
55
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
5 days ago danalvoronov ▴ 10
0
votes
0
replies
55
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
5 days ago k200987 • 0
2
votes
3
replies
151
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 5 days ago by 50k • written 6 days ago by • 0
0
votes
2
replies
756
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 5 days ago by • 0 • written 11 months ago by • 0
0
votes
4
replies
152
views
error running enricher from clusterprofiler
clusterProfiler cluster
6 days ago • updated 5 days ago Yael • 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 5 days ago by • 0 • written 5.2 years ago by ▴ 50
1
vote
2
replies
140
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago Daniel • 0
4
votes
5
replies
343
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 6 days ago Chris ▴ 10
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
2
votes
1
reply
90
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 6 days ago by ★ 1.9k • written 7 days ago by • 0
60 results • Page 1 of 2
Recent ...
Replies
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
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?
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
EMBL Heidelberg, just now
Slovakia, 1 minute ago
Germany, 2 minutes ago
United States, 2 minutes ago
Belgium, 7 minutes ago
Traffic: 770 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