1
vote
3
replies
2.3k
views
Difference between vst() and varianceStabilizingTransform()
DESeq2
written 2.0 years ago by • 0
0
votes
3
replies
759
views
Statistical test
NewWave
written 2.0 years ago by • 0
0
votes
5
replies
1.2k
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by • 0
2
votes
4
replies
1.1k
views
Use of data packages in containers
org.Hs.eg.db
updated 24 months ago by ▴ 760 • written 2.0 years ago by ▴ 20
0
votes
0
replies
961
views
Job: Postdoc position: Spatial and Single-Cell Computational Immunogenomics (@SAiGENCI, Adelaide)
JobPosting
2.0 years ago Stefano Mangiola ▴ 40
0
votes
5
replies
2.5k
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 2.0 years ago by ★ 4.0k • written 2.0 years ago by • 0
2
votes
4
replies
1.2k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 24 months ago by 53k • written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
tximport error with rsem files
rsem tximport
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
0
votes
0
replies
1.2k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
2.0 years ago kyj2226 • 0
2
votes
1
reply
1.5k
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
2
replies
841
views
Running DESeq on normalized data
deseq DESeq2
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
0
votes
1
reply
1.4k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 2.0 years ago by ★ 5.0k • written 7.7 years ago by • 0
0
votes
1
reply
807
views
Error in (function (classes, fdef, mtable) : Function 'raster' tag 'logical' cannot find an inheritance method
NewWave
updated 2.0 years ago by 4.2k • written 2.0 years ago by • 0
0
votes
2
replies
962
views
EBImage - Selecting parameters for x-ray seed size analysis
EBImage
updated 2.0 years ago by ★ 13k • written 2.0 years ago by • 0
1
vote
2
replies
1.9k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
2.0 years ago elgomez • 0
1
vote
4
replies
2.5k
views
BiocParallel serialization errors on Windows
variancePartition BiocParallel
2.0 years ago hayleyw • 0
0
votes
2
replies
1.3k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.0 years ago Luca • 0
0
votes
2
replies
3.0k
views
EnhancedVolcano with labels based on log2 Fold Change
EnhancedVolcano
written 2.0 years ago by • 0
0
votes
2
replies
964
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 2.1 years ago by ▴ 10
0
votes
6
replies
2.2k
views
flowCore >2.0 read.FCS results in $SPILLOVER error when reading certain FCS files (could it be a warning?)
read.FCS flowCore
updated 2.0 years ago by ▴ 360 • written 2.1 years ago by • 0
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 22 months ago by ▴ 10 • written 2.1 years ago by • 0
0
votes
2
replies
1.2k
views
Linear Model Fitting and Colinearity
dese DESeq2
2.1 years ago • updated 2.0 years ago Hugo • 0
0
votes
2
replies
1.2k
views
Error Oligo package asking for pd.2.0 package annotation
oligo
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
4
votes
3
replies
3.1k
views
WGCNA documentation not available
WGCNA
written 2.1 years ago by ▴ 10
1
vote
2
replies
854
views
Assess fit of variance prior
limma
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 30
0
votes
3
replies
2.5k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.8 years ago by • 0
0
votes
5
replies
2.8k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 12.0 years ago by ★ 13k
1
vote
5
replies
2.9k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.9 years ago by ▴ 10
5
votes
1
reply
1.9k
views
News: Bioconductor 3.18 is Released!
Packages Bioconductor Release Software
written 2.2 years ago by 4.2k
5
votes
11
replies
5.4k
views
How to annotate gene names for genomic coordinates?
annotation
written 10.5 years ago by • 0
2
votes
1
reply
650
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
2
replies
880
views
Can't download Bioconductor
BiocVersion
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
vote
2
replies
809
views
Inconsistent results in DiffBind
DiffBind
2.1 years ago • updated 2.0 years ago Sam ▴ 10
3
votes
2
replies
1.4k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
2.1 years ago kyj2226 • 0
1
vote
2
replies
877
views
autonomics: example("read_somascan", package = "autonomics") fails, but not on Bioc check servers
autonomics
2.1 years ago Henrik Bengtsson ★ 2.4k
1
vote
13
replies
2.5k
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 24 months ago by ★ 4.0k • written 2.1 years ago by ▴ 10
2
votes
4
replies
1.8k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
3
replies
930
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
0
votes
4
replies
5.5k
views
Problems with FLOWAI
flowAI
written 4.7 years ago by • 0
0
votes
1
reply
1.7k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
4
replies
6.9k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 2.1 years ago by ▴ 50
5
votes
2
replies
1.6k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
1
reply
2.2k
views
biomaRt_getBM_Failed to collect lazy table
getBM biomaRt
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
2
replies
2.0k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.1 years ago ruba-mahmoud • 0
1
vote
2
replies
916
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ▴ 10 • written 2.1 years ago by • 0
0
votes
2
replies
2.6k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 19 months ago by • 0 • written 3.1 years ago by • 0
0
votes
10
replies
3.9k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 2.1 years ago by • 0
0
votes
6
replies
1.1k
views
rDGIdb package inconsistency with web interface
rDGIdb
2.1 years ago christopherjamessteel1990 • 0
0
votes
2
replies
2.5k
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
0
replies
708
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Catalyst::cluster function does NOT produce the same results when setting seed
visua Visualization CATALYST
2.1 years ago elefth.pavlos ▴ 40
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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