3
votes
18
replies
2.8k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
9 months ago • updated 1 day ago shepherl 3.8k
0
votes
6
replies
544
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
7 weeks ago • updated 6 days ago shepherl 3.8k
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 22 hours ago by • 0 • written 8.8 years ago by ▴ 30
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 5 days ago by • 0 • written 8.0 years ago by ▴ 170
0
votes
4
replies
189
views
DEG with low counts
DESeq2
updated 2 hours ago by 41k • written 4 days ago by • 0
3
votes
3
replies
258
views
permutation test in edgeR
rna-seq edgeR
updated 4 days ago by 50k • written 11 days ago by • 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 days ago by 50k • written 9 days ago by • 0
0
votes
4
replies
116
views
flowStats Search Error
flowStats
updated 2 days ago by 3.8k • written 3 days ago by • 0
4
votes
8
replies
292
views
Memory errors using read.bismark?
dmrseq bsseq
updated 13 hours ago by ▴ 740 • written 8 days ago by • 0
1
vote
2
replies
55
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 34 minutes ago by 65k • written 16 hours ago by • 0
5
votes
13
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 hours ago by 41k • written 4.6 years ago by ▴ 10
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 15 hours ago by • 0 • written 9.1 years ago by ▴ 150
0
votes
3
replies
140
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 20
1
vote
2
replies
78
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
2 days ago Ana • 0
0
votes
1
reply
93
views
SNP locus package for mouse?
SNPlocs packFinder
updated 2 days ago by 65k • written 5 days ago by • 0
0
votes
1
reply
109
views
Bioinformatics student
Des DESeq2
updated 6 days ago by • 0 • written 6 days ago by • 0
2
votes
2
replies
336
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
7 days ago • updated 6 days ago Henry ▴ 10
0
votes
1
reply
667
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 6 days ago by • 0 • written 10 months ago by • 0
2
votes
2
replies
148
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 days ago julia_mcdonough • 0
5
votes
6
replies
377
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 6 days ago by ★ 4.0k • written 9 days ago by ▴ 30
1
vote
2
replies
153
views
Design Matrix within group comparison more than two groups
DESeq2
6 days ago hemantcnaik • 0
2
votes
2
replies
132
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago daniel.carbajo • 0
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 4 days ago by 41k • written 8 days ago by ▴ 10
1
vote
2
replies
226
views
GSVA error
GSVA
5 days ago • updated 3 days ago Alex • 0
0
votes
4
replies
2.8k
views
SingleR Label.Ont
SingleR
updated 3 days ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
107
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 3 days ago by • 0 • written 8 days ago by • 0
2
votes
3
replies
245
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago daniel.carbajo • 0
0
votes
1
reply
108
views
Differentially expressed genes in monocle pseudotime
monocle
updated 3 days ago by 50k • written 5 days ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 2 days ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 1 day ago by • 0 • written 17 months ago by • 0
0
votes
6
replies
153
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
updated 1 day ago by 50k • written 2 days ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 1 day ago by 50k • written 6 months ago by ▴ 10
3
votes
3
replies
136
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
7 days ago • updated 1 day ago jacques.imbert • 0
0
votes
1
reply
74
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by ★ 4.0k • written 2 days ago by • 0
2
votes
3
replies
637
views
DESeq2 setting significant p-value
DESeq2
updated 1 day ago by 41k • written 5.0 years ago by ▴ 10
5
votes
9
replies
795
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 23 hours ago Chris • 0
0
votes
1
reply
73
views
covariate with negative and positive values
DESeq2
updated 21 hours ago by 41k • written 2 days ago by • 0
0
votes
1
reply
54
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 21 hours ago by 41k • written 1 day ago by • 0
0
votes
1
reply
45
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 hours ago by 41k • written 1 day ago by • 0
0
votes
1
reply
48
views
rlog transformation
DESeq2
updated 21 hours ago by 41k • written 1 day ago by • 0
0
votes
1
reply
69
views
Adding columns to DEXSeqResults object
DEXSeq
updated 21 hours ago by ★ 1.9k • written 2 days ago by • 0
0
votes
1
reply
43
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 hours ago by ★ 1.9k • written 1 day ago by • 0
0
votes
4
replies
70
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
18 hours ago • updated 16 hours ago sropri • 0
0
votes
2
replies
886
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by • 0
0
votes
1
reply
56
views
Log-cpm values from limma
limma edgeR RNASeq
updated 4 hours ago by 50k • written 1 day ago by • 0
0
votes
2
replies
43
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
5 hours ago • updated 4 hours ago prity6459 • 0
0
votes
3
replies
65
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 3 hours ago by 50k • written 20 hours ago by • 0
0
votes
3
replies
140
views
FilterByExpr low counts with small sample size
edgeR
updated 3 hours ago by 50k • written 1 day ago by ▴ 10
6
votes
5
replies
374
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 7 weeks ago by • 0
76 results • Page 1 of 2
Recent ...
Replies
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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