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Input Question for deseq.r
RSeqAn
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Nina
• 0
0
votes
1
reply
155
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
quanah.hudson
• 0
3
votes
3
replies
222
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
28 days ago • updated 22 days ago
jacques.imbert
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 22 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 23 days ago
shepherl
3.9k
0
votes
2
replies
930
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 23 days ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 23 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 23 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
0
votes
0
replies
88
views
News:
Services
flowBeads
23 days ago
creativepeptides2018
• 0
0
votes
0
replies
87
views
Enzyme Engineering
BioTIP
23 days ago
bocchemistry
• 0
0
votes
0
replies
86
views
News:
TIDES USA 2024
flowBeads
23 days ago
bocsci11
• 0
0
votes
0
replies
96
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
24 days ago • updated 23 days ago
Maliha Tabassum
• 0
0
votes
4
replies
610
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 24 days ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
200
views
flowStats Search Error
flowStats
updated 24 days ago by
shepherl
3.9k • written 24 days ago by
tholmes
• 0
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
tian.liu0720
• 0
1
vote
2
replies
147
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
24 days ago
Ana
• 0
0
votes
1
reply
125
views
what is the sampleFiles
chipseq
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
zhulin
• 0
0
votes
3
replies
210
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
andrebolerbarros
▴ 20
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
1
vote
1
reply
191
views
Differentially expressed genes in monocle pseudotime
monocle
updated 24 days ago by
Gordon Smyth
50k • written 26 days ago by
kthapa
• 0
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
28 days ago • updated 24 days ago
Henry
▴ 10
2
votes
3
replies
332
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
25 days ago • updated 24 days ago
daniel.carbajo
• 0
0
votes
1
reply
149
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 24 days ago by
kamryncole1963
• 0 • written 29 days ago by
Sara
• 0
0
votes
0
replies
100
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
25 days ago
Virangika
• 0
0
votes
0
replies
76
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
25 days ago
Henry
▴ 10
1
vote
2
replies
583
views
GSVA error
GSVA
26 days ago • updated 25 days ago
Alex
• 0
0
votes
1
reply
135
views
Deseq2 Rlog transformation
DESeq2
updated 25 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Sahar
• 0
1
vote
3
replies
356
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 25 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
28 days ago • updated 25 days ago
daniel.carbajo
• 0
0
votes
1
reply
166
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 4 weeks ago by
Lucie
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 26 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
2
replies
201
views
Design Matrix within group comparison more than two groups
DESeq2
28 days ago • updated 27 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 27 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
441
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 27 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
nhaus
▴ 30
2
votes
2
replies
203
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
28 days ago • updated 27 days ago
julia_mcdonough
• 0
0
votes
1
reply
712
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 27 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
3
votes
1
reply
758
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
2
votes
2
replies
395
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
29 days ago • updated 28 days ago
Henry
▴ 10
0
votes
1
reply
138
views
Bioinformatics student
Des
DESeq2
updated 28 days ago by
hemantcnaik
• 0 • written 28 days ago by
Sahar
• 0
0
votes
0
replies
90
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
28 days ago
shepherl
3.9k
0
votes
0
replies
98
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
28 days ago
Stevie Pederson
• 0
0
votes
1
reply
181
views
DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago
Shefali
• 0
0
votes
4
replies
231
views
Storing directories inside an ExperimentHub package?
ExperimentHub
4 weeks ago • updated 29 days ago
Tim Barry
• 0
8
votes
23
replies
983
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 29 days ago by
Robert Castelo
★ 3.3k • written 4 weeks ago by
Bine
▴ 40
3
votes
6
replies
285
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
29 days ago
nhaus
▴ 30
0
votes
0
replies
106
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
29 days ago
communication
• 0
0
votes
6
replies
344
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 29 days ago by
Tim Peters
▴ 180 • written 5 weeks ago by
s.malik
• 0
0
votes
0
replies
143
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
4 weeks ago
Eryn
• 0
0
votes
0
replies
89
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
4 weeks ago
Dennis
• 0
1
vote
6
replies
506
views
GSVA on separate healthy and disease datasets
GSVA
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Lucy
▴ 60
1,742 results • Page
4 of 35
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Replies
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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