0
votes
0
replies
3
views
Dominance Index for Shotgun Metagenomics Data
microbiome
10 minutes ago Dario Strbenac ★ 1.5k
0
votes
1
reply
74
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 2 hours ago by 50k • written 4 days ago by ▴ 730
0
votes
1
reply
30
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 2 hours ago by ★ 4.0k • written 15 hours ago by • 0
0
votes
6
replies
100
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
updated 13 hours ago by 65k • written 18 hours ago by • 0
2
votes
9
replies
252
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 hours ago by 65k • written 23 hours ago by • 0
0
votes
0
replies
31
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
1 day ago glaciya2018 • 0
1
vote
2
replies
89
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
2 days ago • updated 1 day ago ATpoint ★ 4.0k
0
votes
1
reply
63
views
PCA plot suggestions
DESeq2 PCAtools
updated 21 hours ago by • 0 • written 1 day ago by • 0
0
votes
1
reply
78
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
0
replies
26
views
ATACseq merge peaks
DiffBind
1 day ago Shloka • 0
0
votes
0
replies
22
views
Differential splicing from SGSeq analysis
DEXSeq SGSeq
1 day ago Sara • 0
2
votes
5
replies
147
views
get BM error
ensembldb
updated 1 day ago by 65k • written 2 days ago by • 0
2
votes
5
replies
144
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 19 hours ago by 65k • written 2 days ago by • 0
0
votes
0
replies
31
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago Dario Strbenac ★ 1.5k
1
vote
3
replies
105
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 20
1
vote
4
replies
168
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 5 hours ago winwater0928 • 0
3
votes
1
reply
215
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 40
1
vote
1
reply
83
views
Citation for edgeR user guide
edgeR
updated 2 days ago by 50k • written 2 days ago by ▴ 30
0
votes
7
replies
617
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
8 weeks ago • updated 2 days ago shepherl 3.8k
1
vote
1
reply
62
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 2 days ago by 65k • written 2 days ago by ▴ 10
0
votes
8
replies
236
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 2 days ago by • 0
0
votes
0
replies
28
views
News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
2 days ago info ▴ 10
1
vote
4
replies
138
views
minfi::read.metharray.exp
minfiData minfi
updated 2 days ago by ▴ 780 • written 3 days ago by • 0
0
votes
2
replies
122
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
3 days ago • updated 1 day ago shuwangxinze1996 • 0
1
vote
2
replies
931
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 3 days ago by ▴ 170 • written 14 months ago by ▴ 10
0
votes
1
reply
96
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 3 days ago by 50k • written 3 days ago by • 0
3
votes
3
replies
172
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
1
vote
4
replies
158
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 3 days ago by 65k • written 7 days ago by • 0
0
votes
1
reply
86
views
FDR via q-value
qvalue
updated 3 days ago by 65k • written 6 days ago by • 0
0
votes
5
replies
226
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 1 day ago by 65k • written 4 days ago by • 0
0
votes
2
replies
156
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 days ago • updated 4 days ago catv • 0
0
votes
3
replies
1.1k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 4 days ago by • 0 • written 18 months ago by ▴ 70
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 3 days ago shepherl 3.8k
1
vote
13
replies
278
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
4 days ago • updated 1 day ago fernanda.backsouza ▴ 10
0
votes
0
replies
44
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
5 days ago vaxahey107 • 0
12
votes
12
replies
781
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by ★ 3.3k • written 5 days ago by • 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
5 days ago Sebashish • 0
3
votes
2
replies
164
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 days ago by ★ 3.9k • written 6 days ago by ▴ 10
0
votes
3
replies
103
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by 65k • written 6 days ago by ▴ 30
2
votes
2
replies
143
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 6 days ago by 65k • written 7 days ago by • 0
1
vote
0
replies
208
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
6 days ago BioinfGuru ▴ 30
4
votes
6
replies
334
views
FilterByExpr low counts with small sample size
edgeR
8 days ago • updated 3 days ago Jonathan ▴ 10
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 days ago prity6459 • 0
0
votes
3
replies
130
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 days ago by 50k • written 7 days ago by • 0
3
votes
1
reply
121
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
0
votes
4
replies
134
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
7 days ago sropri • 0
0
votes
1
reply
85
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by ★ 1.9k • written 8 days ago by • 0
0
votes
1
reply
120
views
Adding columns to DEXSeqResults object
DEXSeq
updated 7 days ago by ★ 1.9k • written 9 days ago by • 0
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 7 days ago by 3.8k • written 7 days ago by • 0
0
votes
1
reply
91
views
rlog transformation
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
45,581 results • Page 1 of 912
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
Australia, 1 minute ago
Portugal, 11 minutes ago
Wageningen University, Wageningen, the Netherlands, 37 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
Traffic: 893 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