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Views
Votes
2
votes
2
replies
382
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
21 days ago • updated 20 days ago
Henry
▴ 10
1
vote
3
replies
204
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
494
views
GSVA error
GSVA
19 days ago • updated 17 days ago
Alex
• 0
1
vote
1
reply
154
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 7 days ago by
Gordon Smyth
50k • written 11 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
88
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
Dev
• 0
0
votes
1
reply
120
views
ATACseq merge peaks
DiffBind
updated 7 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
0
votes
1
reply
700
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 20 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
4
replies
190
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
14 days ago
sropri
• 0
0
votes
1
reply
210
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
2
votes
2
replies
168
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
21 days ago • updated 18 days ago
daniel.carbajo
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 16 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
2
replies
918
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
4
replies
5.3k
views
SingleR Label.Ont
SingleR
updated 17 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
3
replies
213
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
2
votes
3
replies
321
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
18 days ago • updated 17 days ago
daniel.carbajo
• 0
1
vote
1
reply
104
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
147
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
zh9118
• 0
0
votes
2
replies
184
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
4 weeks ago • updated 29 days ago
Gimena
• 0
1
vote
3
replies
242
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Shaimaa Gamal
• 0
2
votes
2
replies
186
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 28 days ago by
ATpoint
★ 4.1k • written 28 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
199
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
2 days ago • updated 1 day ago
Yveto
• 0
0
votes
1
reply
136
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 16 days ago by
James W. MacDonald
65k • written 19 days ago by
tian.liu0720
• 0
0
votes
2
replies
175
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 28 days ago
Bhawna
• 0
1
vote
4
replies
462
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
1
vote
2
replies
143
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
9 days ago • updated 8 days ago
ATpoint
★ 4.1k
0
votes
1
reply
236
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 29 days ago by
Tim Peters
▴ 170 • written 29 days ago by
Kim
• 0
1
vote
2
replies
132
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
16 days ago
Ana
• 0
8
votes
23
replies
914
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 21 days ago by
Robert Castelo
★ 3.3k • written 22 days ago by
Bine
▴ 40
1
vote
4
replies
306
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago
winwater0928
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Hong Thu
• 0
0
votes
3
replies
221
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
HAK
• 0
1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 17 days ago by
Gordon Smyth
50k • written 19 days ago by
kthapa
• 0
3
votes
2
replies
206
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 11 days ago by
Guido Hooiveld
★ 3.9k • written 13 days ago by
fernanda.backsouza
▴ 10
3
votes
3
replies
200
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
bioinf
▴ 10
1
vote
1
reply
109
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 7 days ago by
Dario Strbenac
★ 1.5k
1
vote
2
replies
225
views
MethylKit read issue
methylKit
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
5
votes
6
replies
417
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 20 days ago by
ATpoint
★ 4.1k • written 23 days ago by
nhaus
▴ 30
0
votes
1
reply
178
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 24 days ago by
James W. MacDonald
65k • written 25 days ago by
BCS12
• 0
0
votes
1
reply
62
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 hours ago by
Gordon Smyth
50k • written 19 hours ago by
c53aba27
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 15 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
2
replies
186
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Aaliya
• 0
3
votes
1
reply
752
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
0
replies
141
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
25 days ago
arne.sahm
• 0
0
votes
0
replies
142
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
27 days ago
andromeda
• 0
3
votes
0
replies
44
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
1 day ago
shepherl
3.9k
0
votes
0
replies
91
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
8 days ago • updated 4 hours ago
glaciya2018
• 0
0
votes
0
replies
91
views
I am trying to detect alternative splicing.
ASpli
13 days ago
Sebashish
• 0
0
votes
3
replies
98
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
1
vote
13
replies
375
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 8 days ago
fernanda.backsouza
▴ 10
202 results • Page
3 of 5
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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