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3
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18
replies
2.8k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 15 hours ago
shepherl
3.8k
0
votes
4
replies
2.5k
views
SingleR Label.Ont
SingleR
updated 2 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 4 days ago by
Samuel Ahuno
• 0 • written 7.9 years ago by
maltethodberg
▴ 170
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 18 hours ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
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
6
votes
8
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 4 days ago by
gptnederlands.nl
• 0 • written 13 months ago by
Wolfgang Huber
★ 13k
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 8 hours ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 20 hours ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
2
replies
861
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 15 hours ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
5
votes
9
replies
752
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 5 hours ago
Chris
• 0
3
votes
1
reply
730
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
8
votes
23
replies
729
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 6 days ago by
Robert Castelo
★ 3.2k • written 7 days ago by
Bine
▴ 40
0
votes
1
reply
659
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
0
votes
4
replies
549
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 1 day ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
6
replies
539
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
6 weeks ago • updated 5 days ago
shepherl
3.8k
5
votes
6
replies
363
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 days ago by
ATpoint
★ 4.0k • written 8 days ago by
nhaus
▴ 30
2
votes
2
replies
331
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
6 days ago • updated 5 days ago
Henry
▴ 10
1
vote
3
replies
286
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 2 days ago by
Gordon Smyth
50k • written 8 days ago by
Simran
• 0
4
votes
8
replies
276
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 9 hours ago by
Peter Hickey
▴ 710 • written 6 days ago by
Juan Higareda
• 0
3
votes
3
replies
250
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 10 days ago by
Netanel
• 0
2
votes
3
replies
218
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
3 days ago • updated 2 days ago
daniel.carbajo
• 0
1
vote
2
replies
202
views
GSVA error
GSVA
4 days ago • updated 2 days ago
Alex
• 0
3
votes
6
replies
201
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 days ago
nhaus
▴ 30
0
votes
4
replies
175
views
Storing directories inside an ExperimentHub package?
ExperimentHub
7 days ago • updated 6 days ago
Tim Barry
• 0
0
votes
3
replies
158
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
1
vote
1
reply
154
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
1
vote
2
replies
145
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
1
reply
139
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
0
votes
2
replies
135
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
5 days ago • updated 1 day ago
schlumbohm
• 0
2
votes
2
replies
135
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago
julia_mcdonough
• 0
0
votes
3
replies
128
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
0
votes
6
replies
127
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 10 hours ago by
Gordon Smyth
50k • written 22 hours ago by
hortense96
• 0
2
votes
2
replies
125
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 days ago • updated 3 days ago
daniel.carbajo
• 0
2
votes
2
replies
123
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 2 days ago
Henry
▴ 10
0
votes
1
reply
104
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
Lucie
• 0
0
votes
4
replies
104
views
flowStats Search Error
flowStats
updated 1 day ago by
shepherl
3.8k • written 2 days ago by
tholmes
• 0
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
0
votes
2
replies
100
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
updated 2 days ago by
Peter Hickey
▴ 710 • written 5 days ago by
jacques.imbert
• 0
0
votes
1
reply
97
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 2 days ago by
kamryncole1963
• 0 • written 6 days ago by
Sara
• 0
0
votes
1
reply
96
views
Differentially expressed genes in monocle pseudotime
monocle
updated 1 day ago by
Gordon Smyth
50k • written 4 days ago by
kthapa
• 0
0
votes
1
reply
83
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
0
votes
1
reply
81
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
tian.liu0720
• 0
0
votes
0
replies
69
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
6 days ago
communication
• 0
0
votes
0
replies
66
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 days ago
Stevie Pederson
• 0
1
vote
2
replies
64
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
1 day ago
Ana
• 0
0
votes
0
replies
60
views
Cell type in SVD analysis
ChAMP
5 days ago
simleopold11
• 0
0
votes
1
reply
59
views
FilterByExpr low counts with small sample size
edgeR
updated 7 hours ago by
Gordon Smyth
50k • written 16 hours ago by
Jonathan
▴ 10
0
votes
1
reply
60
views
what is the sampleFiles
chipseq
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
zhulin
• 0
66 results • Page
1 of 2
Recent ...
Replies
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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