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4
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6
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482
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago
Jonathan
▴ 10
0
votes
2
replies
153
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
3
replies
219
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
5
votes
3
replies
323
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
4
replies
233
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
0
votes
3
replies
193
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
0
votes
1
reply
169
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 weeks ago by
Alejandro Reyes
★ 1.9k • written 5 weeks ago by
Clyde
• 0
0
votes
0
replies
137
views
Warning while loading DEP package
DEP
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
Namrata
• 0
0
votes
1
reply
160
views
rlog transformation
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
132
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
1
vote
2
replies
762
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
0
votes
1
reply
151
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Brynn
• 0
0
votes
1
reply
171
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
1
vote
2
replies
245
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago
Le
• 0
1
vote
2
replies
183
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago
Sherin
• 0
0
votes
1
reply
113
views
Input Question for deseq.r
RSeqAn
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
0
votes
4
replies
272
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago
lonn
• 0
0
votes
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 29 days ago
hortense96
• 0
0
votes
0
replies
96
views
News:
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flowBeads
4 weeks ago
creativepeptides2018
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0
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94
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Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
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0
replies
99
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News:
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flowBeads
5 weeks ago
bocsci11
• 0
0
votes
0
replies
108
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
5 weeks ago
Maliha Tabassum
• 0
0
votes
4
replies
225
views
flowStats Search Error
flowStats
updated 5 weeks ago by
shepherl
3.9k • written 5 weeks ago by
tholmes
• 0
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 4 weeks ago
shepherl
3.9k
0
votes
1
reply
157
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
tian.liu0720
• 0
1
vote
2
replies
181
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
5 weeks ago
Ana
• 0
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
0
votes
1
reply
138
views
what is the sampleFiles
chipseq
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
zhulin
• 0
1
vote
1
reply
215
views
Differentially expressed genes in monocle pseudotime
monocle
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
kthapa
• 0
4
votes
9
replies
496
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 14 days ago
Juan Higareda
• 0
3
votes
3
replies
249
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
0
votes
1
reply
167
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 5 weeks ago by
kamryncole1963
• 0 • written 5 weeks ago by
Sara
• 0
0
votes
3
replies
236
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
0
replies
109
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
5 weeks ago
Virangika
• 0
0
votes
0
replies
86
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
5 weeks ago
Henry
▴ 10
1
vote
2
replies
268
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
0
votes
4
replies
295
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
1
vote
2
replies
757
views
GSVA error
GSVA
5 weeks ago
Alex
• 0
2
votes
3
replies
350
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
5 weeks ago
daniel.carbajo
• 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
1
vote
3
replies
371
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Simran
• 0
0
votes
1
reply
153
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
0
votes
2
replies
758
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
217
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
2
votes
2
replies
221
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 weeks ago
julia_mcdonough
• 0
2
votes
2
replies
194
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago
Henry
▴ 10
0
votes
1
reply
155
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
0
replies
104
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
2
votes
2
replies
198
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 weeks ago
daniel.carbajo
• 0
0
votes
3
replies
291
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
1,000 results • Page
4 of 20
Recent ...
Replies
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Happiness
• 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
mohammedtoufiq91
▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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