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DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
42
views
News:
Services
flowBeads
3 days ago
creativepeptides2018
• 0
0
votes
0
replies
32
views
Enzyme Engineering
BioTIP
3 days ago
bocchemistry
• 0
0
votes
0
replies
43
views
News:
TIDES USA 2024
flowBeads
3 days ago
bocsci11
• 0
0
votes
0
replies
52
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
3 days ago
Maliha Tabassum
• 0
0
votes
4
replies
556
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 3 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
4
replies
123
views
flowStats Search Error
flowStats
updated 3 days ago by
shepherl
3.8k • written 4 days ago by
tholmes
• 0
0
votes
1
reply
97
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
tian.liu0720
• 0
1
vote
2
replies
86
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
3 days ago
Ana
• 0
0
votes
1
reply
78
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
zhulin
• 0
0
votes
3
replies
149
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
118
views
Differentially expressed genes in monocle pseudotime
monocle
updated 4 days ago by
Gordon Smyth
50k • written 6 days ago by
kthapa
• 0
2
votes
2
replies
137
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 4 days ago
Henry
▴ 10
2
votes
3
replies
264
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
5 days ago • updated 4 days ago
daniel.carbajo
• 0
0
votes
1
reply
109
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 4 days ago by
kamryncole1963
• 0 • written 9 days ago by
Sara
• 0
0
votes
4
replies
2.9k
views
SingleR Label.Ont
SingleR
updated 4 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
63
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 days ago
Virangika
• 0
0
votes
0
replies
48
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 days ago
Henry
▴ 10
1
vote
2
replies
237
views
GSVA error
GSVA
6 days ago • updated 4 days ago
Alex
• 0
0
votes
1
reply
104
views
Deseq2 Rlog transformation
DESeq2
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
Sahar
• 0
1
vote
3
replies
310
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 5 days ago by
Gordon Smyth
50k • written 10 days ago by
Simran
• 0
3
votes
3
replies
265
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 12 days ago by
Netanel
• 0
2
votes
2
replies
136
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
8 days ago • updated 5 days ago
daniel.carbajo
• 0
0
votes
1
reply
115
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Lucie
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 6 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
1
vote
2
replies
156
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 7 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
382
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
2
votes
2
replies
151
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
7 days ago
julia_mcdonough
• 0
0
votes
1
reply
671
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 7 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
3
votes
1
reply
734
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.1 years ago by
Leonardo Collado Torres
★ 1.0k
2
votes
2
replies
342
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 days ago • updated 7 days ago
Henry
▴ 10
0
votes
1
reply
111
views
Bioinformatics student
Des
DESeq2
updated 7 days ago by
hemantcnaik
• 0 • written 7 days ago by
Sahar
• 0
0
votes
0
replies
65
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
7 days ago
shepherl
3.8k
0
votes
0
replies
69
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
8 days ago
Stevie Pederson
• 0
0
votes
1
reply
145
views
DESeq2 gives an error and R crashes
DESeq2
9 days ago • updated 8 days ago
Shefali
• 0
0
votes
4
replies
186
views
Storing directories inside an ExperimentHub package?
ExperimentHub
9 days ago • updated 8 days ago
Tim Barry
• 0
8
votes
23
replies
793
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 8 days ago by
Robert Castelo
★ 3.2k • written 9 days ago by
Bine
▴ 40
3
votes
6
replies
215
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
9 days ago • updated 8 days ago
nhaus
▴ 30
0
votes
0
replies
74
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
8 days ago
communication
• 0
0
votes
6
replies
295
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 9 days ago by
Tim Peters
▴ 170 • written 17 days ago by
s.malik
• 0
0
votes
0
replies
100
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
9 days ago
Eryn
• 0
0
votes
0
replies
68
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
9 days ago
Dennis
• 0
1
vote
6
replies
436
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 days ago by
James W. MacDonald
65k • written 11 days ago by
Lucy
▴ 60
0
votes
1
reply
315
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 9 days ago by
Lluís Revilla Sancho
▴ 730 • written 6 months ago by
karmasstark
• 0
0
votes
1
reply
107
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 9 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Merav
• 0
0
votes
0
replies
82
views
ggtree tip label position (depth)
ggtree
10 days ago
Roope
• 0
0
votes
2
replies
184
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 10 days ago by
Michael Love
41k • written 14 days ago by
nhaus
▴ 30
0
votes
1
reply
131
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Adelaide
• 0
45,551 results • Page
2 of 912
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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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