0
votes
2
replies
959
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 5 months ago by • 0 • written 13 months ago by ▴ 70
2
votes
3
replies
2.8k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 13 months ago by • 0
1
vote
0
replies
806
views
News: Bioconductor Package Download Rate Limitation (HTTP 429)
downloads http429 http Bioconductor
13 months ago shepherl 4.2k
0
votes
3
replies
1.8k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz Saccharomyces_cerevisiae Gviz ideogram
updated 13 months ago by • 0 • written 23 months ago by • 0
0
votes
0
replies
560
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
13 months ago louis.der.hammer • 0
0
votes
9
replies
2.0k
views
'path' must be string
HELP path
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
4
replies
1.2k
views
Recount3: PCR duplicates
pcrduplicates recount3 multimappingreads
updated 13 months ago by ★ 4.9k • written 2.3 years ago by • 0
3
votes
6
replies
1.2k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 13 months ago by • 0
4
votes
3
replies
1.5k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 13 months ago by ▴ 10
0
votes
0
replies
596
views
Error in serialization
scDblFinder BiocParallel
13 months ago Lluís Revilla Sancho ▴ 760
0
votes
1
reply
676
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 13 months ago by 4.2k • written 13 months ago by • 0
4
votes
12
replies
5.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 13 months ago by ▴ 230 • written 21 months ago by ▴ 20
0
votes
3
replies
859
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
13 months ago gallantk5 • 0
0
votes
3
replies
888
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
1
vote
1
reply
1.1k
views
Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
0
votes
0
replies
599
views
Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
13 months ago ramiro.barrantes ▴ 10
0
votes
8
replies
1.7k
views
Error running tximeta
tximeta
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
4
replies
1.3k
views
Generating surrogate variables across multiple variables of interest
sva
13 months ago Robert • 0
1
vote
6
replies
1.1k
views
limma and Syntactically Invalid Factor Values
limma
updated 13 months ago by 52k • written 13 months ago by ★ 1.6k
1
vote
1
reply
956
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
13 months ago Bioinformagician • 0
1
vote
3
replies
846
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
10
replies
1.9k
views
Two treatments, one control
DESeq2 stageR
13 months ago alephreish • 0
0
votes
2
replies
1.9k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
13 months ago Fiona • 0
2
votes
3
replies
854
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 13 months ago by • 0
4
votes
2
replies
922
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 13 months ago by ▴ 180
1
vote
1
reply
1.2k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
618
views
methylKit problem
methylKit
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
1
vote
3
replies
831
views
Create merged ChIP heatmap across conditions
DiffBind profileplyr
updated 13 months ago by ★ 5.2k • written 13 months ago by • 0
0
votes
0
replies
421
views
ASICS to process NMR spectra
ASICS
13 months ago KONG ZHI XIAN • 0
0
votes
0
replies
475
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
13 months ago Kelly • 0
5
votes
3
replies
968
views
Limma comparing gene expression between base line and one treatment
limma
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
1
reply
1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
0
votes
1
reply
508
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
4
votes
9
replies
1.9k
views
Get_interactions is giving the combined score
STRINGdb
updated 13 months ago by • 0 • written 13 months ago by ▴ 20
2
votes
5
replies
995
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 13 months ago by 68k • written 13 months ago by • 0
4
votes
12
replies
1.7k
views
DGE with a Continuous Variable
DESeq2 model
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
4
replies
807
views
Error from runShinyMethyl() - is(object, "shinyMethylSet") is not TRUE
shinyMethyl
updated 13 months ago by 68k • written 13 months ago by • 0
1
vote
5
replies
2.8k
views
ComplexHeatmap - alter legend position
ComplexHeatmap
13 months ago Lucy ▴ 60
4
votes
14
replies
2.4k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 13 months ago by 52k • written 13 months ago by • 0
0
votes
1
reply
517
views
T cell subtype annotation
SingleCellExperiment
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
1
reply
693
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 13 months ago by 68k • written 13 months ago by • 0
6
votes
7
replies
2.0k
views
findOverlaps(), queryHits and subjectHits()
GenomicFiles
updated 13 months ago by 16k • written 13 months ago by • 0
0
votes
0
replies
504
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
13 months ago cereyredondo • 0
0
votes
1
reply
540
views
output from RAIN doesn't look rhythmic
rain
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
0
votes
3
replies
1.7k
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 13 months ago by • 0 • written 2.2 years ago by • 0
1
vote
2
replies
701
views
DESeq2: two conditions two genotypes
DESeq2
13 months ago Rocio • 0
2
votes
4
replies
1.1k
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 13 months ago by • 0
1
vote
4
replies
2.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
13 months ago Lucy ▴ 60
0
votes
2
replies
1.3k
views
Installing Bioconductor
Bioconductor
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
votes
1
reply
530
views
featureCounts from Rsubread
Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
46,612 results • Page 17 of 933
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Awards • All
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Gordon Smyth 52k
Popular Question to littlefishes20 ▴ 10
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to shepherl 4.2k
Locations • All
The city by the bay, 45 minutes ago
Pittsburgh, United States, 1 hour ago
WEHI, Melbourne, Australia, 3 hours ago
United Kingdom, 5 hours ago
San Diego, 5 hours ago
Traffic: 626 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