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Votes
0
votes
0
replies
17
views
rnbeads inference
epigenetics
RnBeads
10 hours ago
nabiyogesh
▴ 10
0
votes
1
reply
33
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 11 hours ago by
James W. MacDonald
62k • written 12 hours ago by
Aleksandra
• 0
1
vote
2
replies
50
views
Sva and batch effect
limma
BatchEffect
sva
updated 10 hours ago by
Gordon Smyth
47k • written 12 hours ago by
Lenny186
• 0
0
votes
0
replies
14
views
model overfitting using OPLS DA for metabolomics analysis
OPLSDA
updated 14 hours ago by
shepherl
3.4k • written 15 hours ago by
kokebhaddis
• 0
0
votes
0
replies
17
views
Numbers of Signaling Pathways?
chemistry
18 hours ago
beikrystal25
• 0
0
votes
0
replies
14
views
Cibersort phenotype file
cibersort
deconvR
immune
18 hours ago
609b0d25
• 0
1
vote
3
replies
61
views
Limma-voom with inverse probability weights (similar to sample weights)
limma
limma-voom
StatisticalMethod
updated 11 hours ago by
Gordon Smyth
47k • written 21 hours ago by
jay
• 0
0
votes
1
reply
27
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 1 day ago by
jeffbrick852
• 0 • written 1 day ago by
liuchangbio
▴ 10
0
votes
1
reply
31
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 12 hours ago by
James W. MacDonald
62k • written 1 day ago by
liuchangbio
▴ 10
0
votes
1
reply
36
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2
featurecounts
updated 1 day ago by
swbarnes2
★ 1.2k • written 1 day ago by
Bo
• 0
0
votes
0
replies
24
views
rtracklayer ignores ranges argument
rtracklayer
1 day ago
Kyle
• 0
0
votes
0
replies
27
views
Changing pathway names in pathway analysis
pathways
Pathways
1 day ago
Katharina
• 0
1
vote
2
replies
73
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
1 day ago
stacy.genovese
• 0
0
votes
0
replies
19
views
Analyze Amplicon Seq results for variants and mutation sites
virus
pcr
amplican
mutations
1 day ago
Sara
• 0
0
votes
1
reply
34
views
DESeq2 parameter infernce
DESeq2
updated 15 hours ago by
Michael Love
39k • written 1 day ago by
BioEpi
• 0
0
votes
1
reply
48
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 15 hours ago by
Michael Love
39k • written 1 day ago by
Laia
▴ 10
0
votes
1
reply
48
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 15 hours ago by
Michael Love
39k • written 1 day ago by
rf
• 0
2
votes
4
replies
74
views
Reproducibility using limma for DE Analysis
limma
seed
DifferentialRegulation
updated 1 day ago by
Gordon Smyth
47k • written 1 day ago by
TSauer
• 0
0
votes
0
replies
20
views
customProDB: error aberrant fasta from SNV
customProDB
1 day ago
finoa.li
• 0
1
vote
1
reply
55
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 1 day ago by
ATpoint
★ 2.1k • written 2 days ago by
luca.s
▴ 40
1
vote
1
reply
46
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
2 days ago
liuchangbio
▴ 10
0
votes
1
reply
38
views
Bioconductor tool for curating annotations?
Annotation
updated 17 hours ago by
Lluís Revilla Sancho
▴ 700 • written 2 days ago by
Charles Plessy
▴ 170
0
votes
1
reply
51
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
updated 2 days ago by
Michael Love
39k • written 2 days ago by
Zainab
• 0
0
votes
0
replies
40
views
Alternatives to perform peptide identification in Bioconductor version '3.16'?
peptide
peptideidentification
rTANDEM
MSGFplus
Alternatives
updated 1 day ago by
shepherl
3.4k • written 4 days ago by
vaddanki
• 0
0
votes
0
replies
46
views
Distance between columns vs distance between rows and SVD
distance
svd
4 days ago
Lenny186
• 0
0
votes
0
replies
32
views
Splicing analysis with ASpli package gives an error when I use binGenome function.
S4Vectors
Aspli
4 days ago
salvocomplicazioni1
• 0
0
votes
1
reply
52
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 1 day ago by
andres.firrincieli
▴ 50 • written 4 days ago by
S
• 0
0
votes
0
replies
32
views
GOplots::GOChord with heatmaps?
GOChord
ggplot2::geom_polygon()
GOplot
ggplot2
4 days ago
adrija.kalvisa
• 0
4
votes
1
reply
81
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 4 days ago by
ATpoint
★ 2.1k • written 4 days ago by
luca.s
▴ 40
0
votes
2
replies
78
views
find tandem repeats in DNA
DNA
repeats
4 days ago
me-nobody
• 0
2
votes
10
replies
234
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR
RNAseq
updated 1 day ago by
Gordon Smyth
47k • written 5 days ago by
k.roelfs
• 0
3
votes
2
replies
73
views
I cannot install annotables package in Rstudio (macOS)
DESeq2
PackageTypeData
package
Annotation
5 days ago • updated 1 day ago
m-bihie
▴ 10
1
vote
3
replies
93
views
transcript name mapping between human and mouse
biomaRt
getLDS
updated 4 days ago by
James W. MacDonald
62k • written 5 days ago by
Eric
• 0
3
votes
5
replies
142
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 5 days ago by
Michael Love
39k • written 6 days ago by
aditya.m
▴ 10
0
votes
0
replies
35
views
Rsubread align every slow in mac but faster in windows
Rsubread
6 days ago
Wei
• 0
0
votes
1
reply
85
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 4 days ago by
Michael Love
39k • written 6 days ago by
m-bihie
▴ 10
0
votes
1
reply
74
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 5 days ago by
ATpoint
★ 2.1k • written 6 days ago by
Danielle
• 0
10
votes
8
replies
235
views
MA plot
MAplot
6 days ago • updated 4 days ago
Nathalie
▴ 10
3
votes
4
replies
112
views
ComplexHeatmap - Default distance and hierarchical clustering methods
ComplexHeatmap
Complex
updated 5 days ago by
elefth.pavlos
▴ 40 • written 6 days ago by
Katharina
• 0
0
votes
3
replies
95
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb
biodbUniprot
updated 5 days ago by
James W. MacDonald
62k • written 6 days ago by
Peter
• 0
0
votes
0
replies
32
views
msa module crash
msa
6 days ago
systems
• 0
0
votes
0
replies
54
views
News:
Seeking members for BioC2023 organizing committee
BioC2023
Bioconductor
community
6 days ago • updated 5 days ago
Maria Doyle
▴ 10
0
votes
1
reply
79
views
about deltaPSI
SpliceWiz
updated 6 days ago by
a.wong
▴ 10 • written 7 days ago by
reza.rahman
• 0
2
votes
3
replies
103
views
How can I draw a barplot of complexheatmap according 'Tumor Type'
heatma
heatmaps
ComplexHeatmap
updated 5 days ago by
elefth.pavlos
▴ 40 • written 7 days ago by
Sooni
▴ 10
2
votes
2
replies
130
views
Volcano Plot in R
cellxgenedp
updated 7 days ago by
Gordon Smyth
47k • written 7 days ago by
Rashi
▴ 10
0
votes
3
replies
130
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
7 days ago • updated 6 days ago
martin.grigorov
• 0
0
votes
1
reply
59
views
convert local downloaded bigwig files to .bed files
BRgen
BRGenomics
updated 7 days ago by
ATpoint
★ 2.1k • written 8 days ago by
kavator
▴ 20
0
votes
1
reply
59
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 8 days ago by
Gordon Smyth
47k • written 8 days ago by
wiscoyogi
• 0
0
votes
1
reply
72
views
NAs in some genes in topTable output
limma
topTable
updated 8 days ago by
Gordon Smyth
47k • written 8 days ago by
thkapell
▴ 10
1
vote
4
replies
140
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
updated 2 days ago by
Jonathan Göke
▴ 30 • written 8 days ago by
Bernardo
• 0
43,725 results • Page
1 of 875
Recent ...
Replies
Comment: Not able to download recount3 data
by
Niveditha
▴ 10
Thank you for the update, Leo. I'll check on this and get back to you in case the issue still persists.
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Sva and batch effect
by
Gordon Smyth
47k
(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…
Comment: Advice for the analysis of microarray data with limma
by
Gordon Smyth
47k
You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…
Votes
Answer: Sva and batch effect
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
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
Answer: Limma-voom with inverse probability weights
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