0
votes
1
reply
17
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated just now by ▴ 30 • written 11 hours ago by ★ 1.5k
0
votes
2
replies
99
views
PCA plot suggestions
DESeq2 PCAtools
updated 7 hours ago by 41k • written 1 day ago by • 0
1
vote
3
replies
90
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 hours ago by 41k • written 1 day ago by • 0
0
votes
1
reply
51
views
ATACseq merge peaks
DiffBind
updated 10 hours ago by ★ 4.0k • written 2 days ago by • 0
0
votes
1
reply
91
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 14 hours ago by 50k • written 4 days ago by ▴ 730
1
vote
7
replies
136
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
1 day ago • updated 5 hours ago pl23 • 0
2
votes
9
replies
272
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 1 day ago by 65k • written 1 day ago by • 0
0
votes
0
replies
35
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
93
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
81
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
0
replies
24
views
Differential splicing from SGSeq analysis
DEXSeq SGSeq
2 days ago Sara • 0
2
votes
5
replies
158
views
get BM error
ensembldb
updated 2 days ago by 65k • written 2 days ago by • 0
2
votes
5
replies
153
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 1 day ago by 65k • written 3 days ago by • 0
0
votes
0
replies
35
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago Dario Strbenac ★ 1.5k
1
vote
3
replies
122
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 20
1
vote
4
replies
190
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 16 hours ago winwater0928 • 0
3
votes
1
reply
229
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by 41k • written 3 days ago by ▴ 40
1
vote
1
reply
94
views
Citation for edgeR user guide
edgeR
updated 3 days ago by 50k • written 3 days ago by ▴ 30
0
votes
7
replies
625
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
8 weeks ago • updated 3 days ago shepherl 3.8k
1
vote
1
reply
65
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 3 days ago by 65k • written 3 days ago by ▴ 10
0
votes
8
replies
245
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 3 days ago by • 0
0
votes
0
replies
30
views
News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
3 days ago info ▴ 10
1
vote
4
replies
145
views
minfi::read.metharray.exp
minfiData minfi
updated 2 days ago by ▴ 780 • written 4 days ago by • 0
0
votes
2
replies
137
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
935
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
99
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 3 days ago by 50k • written 4 days ago by • 0
3
votes
3
replies
174
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
1
vote
4
replies
159
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 4 days ago by 65k • written 8 days ago by • 0
0
votes
1
reply
87
views
FDR via q-value
qvalue
updated 4 days ago by 65k • written 7 days ago by • 0
0
votes
5
replies
233
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 2 days ago by 65k • written 5 days ago by • 0
0
votes
2
replies
160
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 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 4 days ago shepherl 3.8k
1
vote
13
replies
283
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
5 days ago • updated 2 days 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
790
views
Why p value inconsistent when using different number of pathway score?
limma
updated 5 days ago by ★ 3.3k • written 6 days ago by • 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
6 days ago Sebashish • 0
3
votes
2
replies
165
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 days ago by ★ 3.9k • written 7 days ago by ▴ 10
0
votes
3
replies
105
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 7 days ago by 65k • written 7 days ago by ▴ 30
2
votes
2
replies
144
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 7 days ago by 65k • written 8 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
7 days ago BioinfGuru ▴ 30
4
votes
6
replies
347
views
FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago Jonathan ▴ 10
0
votes
2
replies
92
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 days ago prity6459 • 0
0
votes
3
replies
133
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 days ago by 50k • written 8 days ago by • 0
3
votes
1
reply
122
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
139
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
8 days ago sropri • 0
0
votes
1
reply
87
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 8 days ago by ★ 1.9k • written 8 days ago by • 0
0
votes
1
reply
121
views
Adding columns to DEXSeqResults object
DEXSeq
updated 8 days ago by ★ 1.9k • written 10 days ago by • 0
0
votes
0
replies
88
views
Warning while loading DEP package
DEP
updated 8 days ago by 3.8k • written 8 days ago by • 0
0
votes
1
reply
94
views
rlog transformation
DESeq2
updated 8 days ago by 41k • written 8 days ago by • 0
45,581 results • Page 1 of 912
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards • All
Popular Question to Leo Lahti ▴ 30
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
Finland, 6 minutes ago
Canada, 31 minutes ago
France, 32 minutes ago
San Diego, 33 minutes ago
WEHI, Melbourne, Australia, 39 minutes ago
Traffic: 777 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