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0
votes
1
reply
13
views
Different summary() and results() values in DeSeq2
#deseq2
updated 21 minutes ago by
Basti
▴ 540 • written 1 hour ago by
Mafer
• 0
1
vote
3
replies
41
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 1 hour ago by
James W. MacDonald
62k • written 5 hours ago by
Berna
• 0
0
votes
0
replies
22
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
12 hours ago
cathalgking
• 0
0
votes
3
replies
67k
views
Unable to create venndiagram using VennDiagram 1.5.1 package
written 10.2 years ago by
jay kumar
▴ 10
0
votes
0
replies
25
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
15 hours ago
Rihards Saksis
• 0
0
votes
0
replies
15
views
BiocGenerics package: 404 error during R shiny app deployment
BiocGenerics
ddCt
18 hours ago
Arielle
• 0
2
votes
2
replies
52
views
Is ther an annotation package for sheep (Ovis aries)
sheep
database_package
Annotation
1 day ago • updated 3 hours ago
priscilaramosibeas
▴ 10
0
votes
1
reply
44
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
updated 1 day ago by
Wolfgang Huber
13k • written 1 day ago by
Ben J
• 0
0
votes
1
reply
130
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping
AnnotationHub
multiGSEA
16 days ago • updated 1 day ago
Thomas
• 0
0
votes
0
replies
25
views
Categorical or continuous covariates
ALL
The
DifferentialRegulation
PathNet
1 day ago
Mine
• 0
0
votes
0
replies
22
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
1 day ago
Hadar
• 0
2
votes
0
replies
22
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
1 day ago
Robert Castelo
★ 3.0k
0
votes
0
replies
21
views
input for singR function
Seurat_object
singe-cell
singleR
2 days ago
Paria
• 0
4
votes
2
replies
47
views
TPP2D - multicore computing for bootstrapNullAlternativeModel(...)
TPP2D
2 days ago
Tobias
▴ 40
5
votes
1
reply
81
views
Why in Bioconductor community people rarely upvote questions?
bioconductor
updated 2 days ago by
Nathalie
▴ 20 • written 2 days ago by
L
▴ 40
0
votes
0
replies
34
views
Subread installation on Linux ARM64
subread
featureCounts
2 days ago
Keyu
• 0
0
votes
0
replies
30
views
rnbeads inference
epigenetics
RnBeads
2 days ago
nabiyogesh
▴ 10
2
votes
2
replies
91
views
Sva and batch effect
limma
BatchEffect
sva
updated 2 days ago by
Gordon Smyth
47k • written 2 days ago by
Lenny186
• 0
0
votes
1
reply
43
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 2 days ago by
James W. MacDonald
62k • written 2 days ago by
Aleksandra
• 0
0
votes
1
reply
41
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 2 days ago by
James W. MacDonald
62k • written 3 days ago by
liuchangbio
▴ 10
13
votes
10
replies
3.6k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 2 days ago by
Hervé Pagès
16k • written 15 months ago by
sarah.howles
▴ 20
0
votes
1
reply
104
views
msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spectra available
msPurity
Metabolomics
Bioconductor
xcms
spectralMatching
updated 2 days ago by
thomas.nigel.lawson
• 0 • written 3 months ago by
hp71727
▴ 10
0
votes
0
replies
25
views
model overfitting using OPLS DA for metabolomics analysis
OPLSDA
updated 2 days ago by
shepherl
3.4k • written 2 days ago by
kokebhaddis
• 0
0
votes
2
replies
63
views
DESeq2 parameter infernce
DESeq2
3 days ago • updated 1 day ago
BioEpi
• 0
0
votes
1
reply
56
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 3 days ago by
Michael Love
39k • written 4 days ago by
Laia
▴ 10
0
votes
1
reply
68
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 3 days ago by
Michael Love
39k • written 4 days ago by
rf
• 0
1
vote
0
replies
150
views
News:
Join the Community Advisory Board -- upcoming elections -- deadline Today
Bioconductor
CAB
bioconductoroversight
community
7 weeks ago • updated 3 days ago
shepherl
3.4k
0
votes
0
replies
24
views
Numbers of Signaling Pathways?
chemistry
3 days ago
beikrystal25
• 0
0
votes
0
replies
27
views
Cibersort phenotype file
cibersort
deconvR
immune
3 days ago
609b0d25
• 0
1
vote
3
replies
79
views
Limma-voom with inverse probability weights (similar to sample weights)
limma
limma-voom
StatisticalMethod
updated 2 days ago by
Gordon Smyth
47k • written 3 days ago by
jay
• 0
0
votes
1
reply
36
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 3 days ago by
jeffbrick852
• 0 • written 3 days ago by
liuchangbio
▴ 10
0
votes
1
reply
47
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 3 days ago by
swbarnes2
★ 1.2k • written 3 days ago by
Bo
• 0
0
votes
0
replies
30
views
rtracklayer ignores ranges argument
rtracklayer
3 days ago
Kyle
• 0
0
votes
0
replies
30
views
Changing pathway names in pathway analysis
pathways
Pathways
3 days ago
Katharina
• 0
1
vote
2
replies
88
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
3 days ago
stacy.genovese
• 0
0
votes
0
replies
25
views
Analyze Amplicon Seq results for variants and mutation sites
virus
pcr
amplican
mutations
3 days ago
Sara
• 0
1
vote
1
reply
70
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 4 days ago by
ATpoint
★ 2.1k • written 4 days ago by
luca.s
▴ 40
2
votes
4
replies
95
views
Reproducibility using limma for DE Analysis
limma
seed
DifferentialRegulation
updated 3 days ago by
Gordon Smyth
47k • written 4 days ago by
TSauer
• 0
0
votes
0
replies
28
views
customProDB: error aberrant fasta from SNV
customProDB
4 days ago
finoa.li
• 0
1
vote
1
reply
54
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
4 days ago
liuchangbio
▴ 10
0
votes
1
reply
53
views
Bioconductor tool for curating annotations?
Annotation
updated 3 days ago by
Lluís Revilla Sancho
▴ 700 • written 4 days ago by
Charles Plessy
▴ 170
0
votes
1
reply
58
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
updated 4 days ago by
Michael Love
39k • written 5 days ago by
Zainab
• 0
0
votes
0
replies
43
views
Alternatives to perform peptide identification in Bioconductor version '3.16'?
peptide
peptideidentification
rTANDEM
MSGFplus
Alternatives
updated 4 days ago by
shepherl
3.4k • written 6 days ago by
vaddanki
• 0
0
votes
0
replies
50
views
Distance between columns vs distance between rows and SVD
distance
svd
6 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
82
views
find tandem repeats in DNA
DNA
repeats
7 days ago • updated 6 days ago
me-nobody
• 0
0
votes
0
replies
38
views
Splicing analysis with ASpli package gives an error when I use binGenome function.
S4Vectors
Aspli
6 days ago
salvocomplicazioni1
• 0
4
votes
1
reply
95
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 6 days ago by
ATpoint
★ 2.1k • written 7 days ago by
luca.s
▴ 40
0
votes
1
reply
60
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 4 days ago by
andres.firrincieli
▴ 50 • written 7 days ago by
S
• 0
0
votes
0
replies
37
views
GOplots::GOChord with heatmaps?
GOChord
ggplot2::geom_polygon()
GOplot
ggplot2
7 days ago
adrija.kalvisa
• 0
217 results • Page
1 of 5
Recent ...
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Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2
by
Basti
▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Comment: Atena package - error (new user)
by
beatriz.calvo
▴ 30
Hi Lalani, We have fixed the bug that lead to the error. The new version of the package (with the bug fixed) will be available in 24-48h. …
Answer: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
You cannot use `mas5calls` on a miRNA-4_0 array. There are no MM probes on that array, so it is not possible to get MAS-5.0 calls, because …
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
As mentioned before, this answer did not help me.
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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