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3
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18
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2.9k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 13 days ago
shepherl
3.8k
0
votes
2
replies
902
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 13 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 13 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 13 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
69
views
News:
Services
flowBeads
13 days ago
creativepeptides2018
• 0
0
votes
0
replies
71
views
Enzyme Engineering
BioTIP
13 days ago
bocchemistry
• 0
0
votes
0
replies
69
views
News:
TIDES USA 2024
flowBeads
14 days ago
bocsci11
• 0
0
votes
0
replies
85
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
14 days ago
Maliha Tabassum
• 0
0
votes
4
replies
588
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 14 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
173
views
flowStats Search Error
flowStats
updated 14 days ago by
shepherl
3.8k • written 15 days ago by
tholmes
• 0
0
votes
1
reply
131
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 14 days ago by
James W. MacDonald
65k • written 17 days ago by
tian.liu0720
• 0
1
vote
2
replies
126
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
14 days ago
Ana
• 0
0
votes
1
reply
110
views
what is the sampleFiles
chipseq
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
zhulin
• 0
0
votes
3
replies
190
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 14 days ago by
Michael Love
41k • written 15 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
1
vote
1
reply
174
views
Differentially expressed genes in monocle pseudotime
monocle
updated 14 days ago by
Gordon Smyth
50k • written 17 days ago by
kthapa
• 0
2
votes
2
replies
160
views
[DiffBind] Obtaining normalization factors
DiffBind
18 days ago • updated 15 days ago
Henry
▴ 10
2
votes
3
replies
308
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
16 days ago • updated 15 days ago
daniel.carbajo
• 0
0
votes
1
reply
133
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 15 days ago by
kamryncole1963
• 0 • written 19 days ago by
Sara
• 0
0
votes
4
replies
4.9k
views
SingleR Label.Ont
SingleR
updated 15 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
85
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
15 days ago
Virangika
• 0
0
votes
0
replies
63
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
15 days ago
Henry
▴ 10
1
vote
2
replies
460
views
GSVA error
GSVA
16 days ago • updated 15 days ago
Alex
• 0
0
votes
1
reply
120
views
Deseq2 Rlog transformation
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Sahar
• 0
1
vote
3
replies
337
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 15 days ago by
Gordon Smyth
50k • written 21 days ago by
Simran
• 0
2
votes
2
replies
161
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
18 days ago • updated 16 days ago
daniel.carbajo
• 0
0
votes
1
reply
148
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 16 days ago by
Guido Hooiveld
★ 3.9k • written 20 days ago by
Lucie
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 17 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
2
replies
182
views
Design Matrix within group comparison more than two groups
DESeq2
18 days ago • updated 17 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 17 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
411
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 18 days ago by
ATpoint
★ 4.1k • written 21 days ago by
nhaus
▴ 30
2
votes
2
replies
183
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
18 days ago
julia_mcdonough
• 0
0
votes
1
reply
693
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 18 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
3
votes
1
reply
751
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
375
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
19 days ago • updated 18 days ago
Henry
▴ 10
0
votes
1
reply
126
views
Bioinformatics student
Des
DESeq2
updated 18 days ago by
hemantcnaik
• 0 • written 18 days ago by
Sahar
• 0
0
votes
0
replies
78
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
18 days ago
shepherl
3.8k
0
votes
0
replies
85
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
19 days ago
Stevie Pederson
• 0
0
votes
1
reply
166
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago
Shefali
• 0
0
votes
4
replies
216
views
Storing directories inside an ExperimentHub package?
ExperimentHub
20 days ago • updated 19 days ago
Tim Barry
• 0
8
votes
23
replies
899
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 19 days ago by
Robert Castelo
★ 3.3k • written 20 days ago by
Bine
▴ 40
3
votes
6
replies
259
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
19 days ago
nhaus
▴ 30
0
votes
0
replies
93
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
19 days ago
communication
• 0
0
votes
6
replies
319
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 20 days ago by
Tim Peters
▴ 170 • written 28 days ago by
s.malik
• 0
0
votes
0
replies
122
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
20 days ago
Eryn
• 0
0
votes
0
replies
81
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
20 days ago
Dennis
• 0
1
vote
6
replies
473
views
GSVA on separate healthy and disease datasets
GSVA
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
Lucy
▴ 60
0
votes
1
reply
331
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 20 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
1
reply
130
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Merav
• 0
0
votes
0
replies
103
views
ggtree tip label position (depth)
ggtree
21 days ago
Roope
• 0
1,000 results • Page
3 of 20
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
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Ian Donaldson
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junhui.li11
• 0
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to
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65k
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• 0
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