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0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
22 days ago • updated 21 days ago
kcarey
• 0
0
votes
6
replies
313
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 20 days ago by
swbarnes2
★ 1.4k • written 21 days ago by
arfranco
▴ 130
0
votes
5
replies
243
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 15 hours ago by
xuz
• 0 • written 2 days ago by
minardsmitha
▴ 10
0
votes
2
replies
145
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
7 days ago
makala
• 0
0
votes
3
replies
196
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 23 days ago by
Alejandro Reyes
★ 1.9k • written 5 weeks ago by
Alessia
• 0
0
votes
8
replies
561
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 9 days ago by
BioinfGuru
▴ 30 • written 10 days ago by
Eric Katagirya
• 0
0
votes
0
replies
81
views
Treeio as.treedata function seq lenght error
treeio
16 days ago
nromerov
• 0
0
votes
3
replies
103
views
pathview error
KEGGgraph
KEGG
updated 22 hours ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Fara
• 0
0
votes
0
replies
102
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
29 days ago • updated 25 days ago
Sara
• 0
0
votes
1
reply
170
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
kcarey
• 0
0
votes
4
replies
388
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 12 days ago by
Ziliang
• 0 • written 22 days ago by
Ian D.
▴ 70
0
votes
0
replies
100
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
24 days ago
Chris
▴ 10
0
votes
2
replies
760
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 8 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 18 days ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
149
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
28 days ago • updated 20 days ago
glaciya2018
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
3 days ago
shahrozimmac
0
0
votes
0
replies
91
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
14 days ago
neilzhao
▴ 30
0
votes
1
reply
121
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 14 days ago by
ATpoint
★ 4.2k • written 14 days ago by
sajadahmad41454
• 0
0
votes
4
replies
177
views
error running enricher from clusterprofiler
clusterProfiler
cluster
8 days ago
Yael
• 0
0
votes
5
replies
341
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
Gayatri
• 0
0
votes
0
replies
15
views
News:
Bioconductor Build System
Builds
Bioconductor
12 hours ago
shepherl
3.9k
0
votes
1
reply
150
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 21 days ago by
4r-rtg
• 0
0
votes
0
replies
102
views
flowStats for CyTOF
flowStats
21 days ago
tholmes
• 0
0
votes
2
replies
279
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
4 weeks ago • updated 29 days ago
shuwangxinze1996
• 0
0
votes
1
reply
132
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 23 days ago by
shepherl
3.9k • written 24 days ago by
bounlu
• 0
0
votes
1
reply
195
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 13 days ago by
ATpoint
★ 4.2k • written 13 days ago by
sajadahmad41454
• 0
0
votes
0
replies
143
views
Empty table plot using plotGseaTable()
fgsea
22 days ago • updated 20 days ago
Chris
▴ 10
0
votes
4
replies
1.3k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 6 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 13 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
0
replies
36
views
Conditional analysis
GENESIS
2 days ago
SuperDad
• 0
0
votes
0
replies
67
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
8 days ago
danalvoronov
▴ 10
0
votes
3
replies
285
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 23 days ago by
James W. MacDonald
66k • written 24 days ago by
SSSJec
• 0
0
votes
0
replies
56
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
5 days ago • updated 4 days ago
Abiologist
• 0
0
votes
0
replies
126
views
dba.plotProfile() plotting and interpretation
DiffBind
20 days ago
Henry
▴ 10
0
votes
1
reply
120
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 9 days ago by
Michael Love
42k • written 10 days ago by
piemmea
• 0
0
votes
3
replies
11k
views
SingleR Label.Ont
SingleR
updated 12 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
3
replies
139
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 6 days ago by
damian.szk
▴ 80 • written 6 days ago by
ninidea
• 0
0
votes
2
replies
234
views
Visium RNA
metaMSdata
written 9 weeks ago by
Karlison
• 0
0
votes
2
replies
233
views
PCA plot suggestions
DESeq2
PCAtools
updated 27 days ago by
Michael Love
42k • written 29 days ago by
Aaliya
• 0
0
votes
3
replies
240
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 21 days ago by
ATpoint
★ 4.2k • written 22 days ago by
james.zhang20
• 0
0
votes
1
reply
143
views
putting my own expression data in deseq2
DESeq2
updated 23 days ago by
ATpoint
★ 4.2k • written 23 days ago by
Dev
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
7 days ago
oliverelijhan
0
0
votes
0
replies
65
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
8 days ago
k200987
• 0
0
votes
3
replies
241
views
Couldn't connect to server while using "pathways"
graphite
updated 17 days ago by
Michael Love
42k • written 18 days ago by
fduguchunhui
• 0
0
votes
1
reply
64
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 3 days ago by
ATpoint
★ 4.2k • written 3 days ago by
V_Vibes
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 17 days ago by
Caio
• 0 • written 13.2 years ago by
boczniak767
▴ 720
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 9 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
1
reply
270
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 23 days ago by
James W. MacDonald
66k • written 24 days ago by
SSSJec
• 0
0
votes
0
replies
99
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
23 days ago
Maria Doyle
▴ 70
0
votes
0
replies
35
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
2 days ago
Raghad
• 0
184 results • Page
3 of 4
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
by
jovel_juan
▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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50k
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★ 4.2k
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▴ 720
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