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0
votes
0
replies
4
views
rtracklayer ignores ranges argument
rtracklayer
31 minutes ago
Kyle
• 0
0
votes
0
replies
15
views
Changing pathway names in pathway analysis
pathways
Pathways
5 hours ago
Katharina
• 0
1
vote
2
replies
56
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
6 hours ago • updated 5 hours ago
stacy.genovese
• 0
0
votes
0
replies
14
views
Analyze Amplicon Seq results for variants and mutation sites
virus
pcr
amplican
mutations
6 hours ago
Sara
• 0
0
votes
0
replies
14
views
DESeq2 parameter infernce
DESeq2parameterinfernce
6 hours ago
BioEpi
• 0
1
vote
1
reply
45
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 9 hours ago by
ATpoint
★ 2.1k • written 17 hours ago by
luca.s
▴ 40
0
votes
0
replies
20
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
11 hours ago
Laia
▴ 10
0
votes
0
replies
20
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
12 hours ago
rf
• 0
2
votes
4
replies
66
views
Reproducibility using limma for DE Analysis
limma
seed
DifferentialRegulation
15 hours ago • updated 13 hours ago
TSauer
• 0
0
votes
0
replies
14
views
customProDB: error aberrant fasta from SNV
customProDB
15 hours ago
finoa.li
• 0
0
votes
1
reply
27
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
20 hours ago • updated 19 hours ago
liuchangbio
• 0
0
votes
0
replies
24
views
Bioconductor tool for curating annotations?
Annotation
21 hours ago
Charles Plessy
▴ 170
0
votes
1
reply
47
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
updated 1 day ago by
Michael Love
39k • written 1 day ago by
Zainab
• 0
0
votes
0
replies
35
views
Alternatives to perform peptide identification in Bioconductor version '3.16'?
peptide
peptideidentification
rTANDEM
MSGFplus
Alternatives
updated 10 hours ago by
shepherl
3.4k • written 2 days ago by
vaddanki
• 0
0
votes
0
replies
41
views
Distance between columns vs distance between rows and SVD
distance
svd
3 days ago
Lenny186
• 0
0
votes
3
replies
1.3k
views
Which version of DESeq2 for R 4.1.2 64bit
DESeq2
written 12 months ago by
pam
• 0
0
votes
2
replies
75
views
find tandem repeats in DNA
DNA
repeats
3 days ago
me-nobody
• 0
0
votes
0
replies
31
views
Splicing analysis with ASpli package gives an error when I use binGenome function.
S4Vectors
Aspli
3 days ago
salvocomplicazioni1
• 0
4
votes
1
reply
76
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 3 days ago by
ATpoint
★ 2.1k • written 3 days ago by
luca.s
▴ 40
0
votes
1
reply
50
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 hours ago by
andres.firrincieli
▴ 50 • written 3 days ago by
S
• 0
0
votes
0
replies
29
views
GOplots::GOChord with heatmaps?
GOChord
ggplot2::geom_polygon()
GOplot
ggplot2
3 days ago
adrija.kalvisa
• 0
2
votes
10
replies
217
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR
RNAseq
updated 1 hour ago by
Gordon Smyth
47k • written 4 days ago by
k.roelfs
• 0
10
votes
8
replies
214
views
MA plot
MAplot
5 days ago • updated 3 days ago
Nathalie
▴ 10
1
vote
3
replies
90
views
transcript name mapping between human and mouse
biomaRt
getLDS
updated 3 days ago by
James W. MacDonald
62k • written 4 days ago by
Eric
• 0
3
votes
2
replies
69
views
I cannot install annotables package in Rstudio (macOS)
DESeq2
PackageTypeData
package
Annotation
4 days ago • updated 9 hours ago
m-bihie
▴ 10
2
votes
3
replies
102
views
How can I draw a barplot of complexheatmap according 'Tumor Type'
heatma
heatmaps
ComplexHeatmap
updated 4 days ago by
elefth.pavlos
▴ 40 • written 5 days ago by
Sooni
▴ 10
3
votes
5
replies
139
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 4 days ago by
Michael Love
39k • written 4 days ago by
aditya.m
▴ 10
0
votes
0
replies
34
views
Rsubread align every slow in mac but faster in windows
Rsubread
4 days ago
Wei
• 0
3
votes
4
replies
110
views
ComplexHeatmap - Default distance and hierarchical clustering methods
ComplexHeatmap
Complex
updated 4 days ago by
elefth.pavlos
▴ 40 • written 5 days ago by
Katharina
• 0
0
votes
1
reply
80
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 3 days ago by
Michael Love
39k • written 5 days ago by
m-bihie
▴ 10
0
votes
1
reply
66
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 4 days ago by
ATpoint
★ 2.1k • written 5 days ago by
Danielle
• 0
0
votes
3
replies
91
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb
biodbUniprot
updated 4 days ago by
James W. MacDonald
62k • written 5 days ago by
Peter
• 0
0
votes
0
replies
31
views
msa module crash
msa
5 days ago
systems
• 0
0
votes
0
replies
53
views
News:
Seeking members for BioC2023 organizing committee
BioC2023
Bioconductor
community
5 days ago • updated 4 days ago
Maria Doyle
▴ 10
0
votes
1
reply
71
views
about deltaPSI
SpliceWiz
updated 5 days ago by
a.wong
▴ 10 • written 5 days ago by
reza.rahman
• 0
2
votes
2
replies
120
views
Volcano Plot in R
cellxgenedp
updated 5 days ago by
Gordon Smyth
47k • written 6 days ago by
Rashi
▴ 10
0
votes
1
reply
866
views
limma: decideTests
affy
limma
affy
limma
updated 5 days ago by
Gordon Smyth
47k • written 15.1 years ago by
Al Ivens
▴ 270
0
votes
3
replies
124
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
6 days ago • updated 5 days ago
martin.grigorov
• 0
1
vote
0
replies
121
views
News:
Join the Community Advisory Board -- upcoming elections -- deadline January 31st
Bioconductor
CAB
bioconductoroversight
community
6 weeks ago • updated 6 days ago
shepherl
3.4k
0
votes
1
reply
56
views
convert local downloaded bigwig files to .bed files
BRgen
BRGenomics
updated 6 days ago by
ATpoint
★ 2.1k • written 6 days ago by
kavator
▴ 20
0
votes
1
reply
68
views
NAs in some genes in topTable output
limma
topTable
updated 6 days ago by
Gordon Smyth
47k • written 6 days ago by
thkapell
▴ 10
0
votes
1
reply
56
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 6 days ago by
Gordon Smyth
47k • written 6 days ago by
wiscoyogi
• 0
0
votes
1
reply
88
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 6 days ago by
Michael Love
39k • written 11 days ago by
joanna
• 0
0
votes
1
reply
75
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 6 days ago by
Michael Love
39k • written 7 days ago by
kalavattam
• 0
1
vote
4
replies
133
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
updated 17 hours ago by
Jonathan Göke
▴ 30 • written 7 days ago by
Bernardo
• 0
0
votes
1
reply
61
views
Subset count data in DGEList using edgeR/DESeq2
edgeR
DMR
updated 6 days ago by
Michael Love
39k • written 7 days ago by
Fiona
• 0
0
votes
2
replies
75
views
scanBam
Rsamtools
Rsam
updated 6 days ago by
Martin Morgan
25k • written 8 days ago by
jojo.valensi
• 0
2
votes
3
replies
104
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db
AnnotationDbi
updated 7 days ago by
James W. MacDonald
62k • written 7 days ago by
harish
• 0
0
votes
0
replies
23
views
INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
7 days ago
MK
• 0
0
votes
2
replies
89
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 7 days ago by
Rory Stark
★ 4.6k • written 11 days ago by
slrpatty
• 0
43,715 results • Page
1 of 875
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
`PoolStatus` just indicates whether a sample is a pool or not, i.e., the first option.
Comment: How to map geneIds to ENTREZIDs
by
stacy.genovese
• 0
James - I wish I knew where you lived so I could buy you a beer! Thank you so much for your help. I'm going to work now on converting th…
Answer: How to map geneIds to ENTREZIDs
by
James W. MacDonald
62k
You are close. But note that the geneIds in your `GRanges` object are NCBI Gene IDs, which used to be called Entrez Gene IDs, and which are…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Just so I don't make a mistake, do I just tell voomLmFit if a sample is a pool or a replicate independent of each group, or do I have to sp…
Comment: I cannot install annotables package in Rstudio (macOS)
by
m-bihie
▴ 10
thanks, this worked!
Votes
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: How to map geneIds to ENTREZIDs
Comment: ComplexHeatmap - Default distance and hierarchical clustering methods
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
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▴ 30
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3.4k
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