0
votes
2
replies
71
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
13 hours ago • updated 10 hours ago makala • 0
2
votes
2
replies
261
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 12 hours ago Matthew Thornton ▴ 360
0
votes
0
replies
28
views
determine k during RUVSeq
RUVSeq RUVnormalize
16 hours ago Ειρήνη • 0
2
votes
3
replies
73
views
Problem installing ChAMP on a MacBook
ChAMP
updated 17 hours ago by 3.9k • written 1 day ago by • 0
0
votes
0
replies
25
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
17 hours ago Shaimaa Gamal • 0
0
votes
0
replies
12
views
Spam: Unveiling Unmatched Best Custom Patches
SIMAT
17 hours ago oliverelijhan 0
0
votes
0
replies
37
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
20 hours ago Anton01 • 0
0
votes
0
replies
24
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
1 day ago danalvoronov ▴ 10
0
votes
0
replies
26
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
1 day ago k200987 • 0
1
vote
4
replies
154
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
updated 1 day ago by 690 • written 1 day ago by ▴ 10
0
votes
4
replies
105
views
error running enricher from clusterprofiler
clusterProfiler cluster
1 day ago Yael • 0
2
votes
3
replies
101
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
2
votes
1
reply
55
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by ★ 1.9k • written 3 days ago by • 0
4
votes
9
replies
212
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 16 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
0
replies
25
views
Difference in Contrast in DiffBind
DiffBind
1 day ago zzrammal • 0
1
vote
2
replies
73
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
1 day ago Patadù ▴ 10
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 220 • written 6.7 years ago by ▴ 80
0
votes
3
replies
87
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 1 day ago by 42k • written 2 days ago by • 0
0
votes
2
replies
105
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 2 days ago by ▴ 10 • written 4 days ago by • 0
1
vote
0
replies
314
views
News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
7 weeks ago • updated 2 days ago shepherl 3.9k
1
vote
2
replies
105
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago Daniel • 0
0
votes
1
reply
73
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 2 days ago by 42k • written 3 days ago by • 0
0
votes
1
reply
52
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA starBase ceRNA WebAPI ENCORI
2 days ago • updated 1 day ago Bhavya • 0
1
vote
0
replies
44
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
2 days ago Aleena ▴ 30
0
votes
0
replies
41
views
QSEA- Extraction of Normalized methylation across the samples
qsea ngsReports correlation
3 days ago Researcher • 0
0
votes
8
replies
460
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 2 days ago by ▴ 30 • written 3 days ago by • 0
1
vote
3
replies
215
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 2 days ago by 50k • written 3 days ago by • 0
3
votes
4
replies
264
views
Store output of matchPWM()
biostrings Biostrings
15 days ago • updated 3 days ago mat149 ▴ 70
1
vote
2
replies
168
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 10 hours ago BioinfGuru ▴ 30
0
votes
2
replies
77
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
3 days ago • updated 2 days ago Yveto • 0
0
votes
1
reply
101
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 3 days ago by ★ 4.0k • written 4 days ago by • 0
0
votes
3
replies
137
views
ChAMP installation issue
Cha ChAMP
4 days ago • updated 2 days ago e1271094 • 0
0
votes
3
replies
8.4k
views
SingleR Label.Ont
SingleR
updated 5 days ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
152
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
2
votes
7
replies
353
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 days ago • updated 5 days ago sajadahmad41454 • 0
2
votes
2
replies
263
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago zzrammal • 0
3
votes
10
replies
433
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 6 days ago by 65k • written 9 days ago by • 0
4
votes
5
replies
310
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
11 days ago • updated 1 day ago Chris ▴ 10
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 2 days ago by 42k • written 15 months ago by • 0
0
votes
4
replies
358
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by • 0 • written 15 days ago by ▴ 70
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by ▴ 30
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 days ago by 50k • written 28 days ago by • 0
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 1 day ago by • 0 • written 11 months ago by • 0
7
votes
37
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 7 hours ago by • 0 • written 5.5 years ago by ★ 4.0k
1
vote
5
replies
513
views
Can't post a question containing code?
Bioconductor
updated 6 days ago by • 0 • written 3 months ago by ▴ 10
0
votes
2
replies
941
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 1 day ago by • 0 • written 17 months ago by • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 6 days ago by • 0 • written 15 months ago by ▴ 10
2
votes
3
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 3 days ago by • 0 • written 3.6 years ago by ▴ 60
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 1 day ago by • 0 • written 5.2 years ago by ▴ 50
49 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Awards • All
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Michael Love 42k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to boczniak767 ▴ 720
Locations • All
United States, 10 minutes ago
WEHI, Melbourne, Australia, 14 minutes ago
India, 31 minutes ago
Melbourne, Australia, 41 minutes ago
Singapore, 56 minutes ago
Traffic: 420 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