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0
votes
9
replies
2.3k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.1 years ago
nromerov
• 0
0
votes
3
replies
1.2k
views
Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
2.1 years ago
claire
• 0
0
votes
2
replies
859
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.1 years ago
davca
• 0
0
votes
0
replies
737
views
Cannot read biom file in R
RESOLVE
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Jashvant Kumar
• 0
1
vote
1
reply
645
views
Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Durga
▴ 10
2
votes
3
replies
1.6k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
2.1 years ago
Karthik
• 0
2
votes
1
reply
758
views
DataFrame Printing User Control
S4Vectors
updated 2.1 years ago by
Hervé Pagès
16k • written 2.1 years ago by
Dario Strbenac
★ 1.6k
3
votes
2
replies
1.2k
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl
biomaRt
2.1 years ago
henrydionne
▴ 10
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
2.1 years ago
pl23
• 0
0
votes
0
replies
649
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
2.1 years ago
Joshua
• 0
0
votes
1
reply
934
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Ana
• 0
2
votes
5
replies
4.6k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 21 months ago by
damian.szk
▴ 110 • written 2.1 years ago by
Abhishek
• 0
0
votes
2
replies
990
views
FlowSOM error system.file()
FlowSOM
updated 2.1 years ago by
SamGG
▴ 360 • written 2.1 years ago by
agus_rizzo
• 0
1
vote
2
replies
2.6k
views
How to find stop codons for a list of genes
stopcodon
biomaRt
2.1 years ago
Marek Gierlinski
▴ 30
2
votes
28
replies
7.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 2.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Manmohit
▴ 10
0
votes
1
reply
811
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Pez
▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
2.1 years ago
Manthos
• 0
1
vote
4
replies
1.5k
views
Can DESeq2 be used to compare groups of genes?
DESeq2
2.1 years ago
pl23
• 0
0
votes
4
replies
1.0k
views
ATACseqTFEA - preparebindingSites() for whole genome?
ATACseqTFEA
updated 23 months ago by
Ou, Jianhong
★ 1.3k • written 2.1 years ago by
jfmay
• 0
0
votes
1
reply
764
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
inna.gur
• 0
0
votes
2
replies
1.0k
views
Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware
SingleCellData
annotationTools
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
yw24418
• 0
0
votes
4
replies
1.6k
views
rhdf5: error trying to access files from S3 Cloud from NASA earthaccess
rhdf5
2.1 years ago
Caio
• 0
1
vote
7
replies
10k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 22 months ago by
Hervé Pagès
16k • written 2.2 years ago by
inzirio
▴ 10
2
votes
1
reply
1.4k
views
ChAMP can't be found in Bioc3.18?
ChAMP
2.1 years ago
ramonfallon
▴ 20
0
votes
6
replies
3.7k
views
Error when Installing BioConductor Package ('affy')
Bioconductor
Install
affy
updated 2.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
laujihen
• 0
0
votes
0
replies
850
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
2.1 years ago
vasily.dobrovolsky
• 0
0
votes
1
reply
801
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
glopez
• 0
2
votes
2
replies
1.2k
views
Predicting missing values splines DESeq2
deseq
DESeq2
2.1 years ago
georgii.vdovin
• 0
0
votes
0
replies
627
views
GaussNorm fails to recognize flowFrames in flowSet as individual elements
flowStats
2.1 years ago
mikkel.byrdal
• 0
1
vote
3
replies
2.7k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 2.1 years ago by
Robert Ivanek
▴ 750 • written 4.7 years ago by
ltzhou
• 0
2
votes
0
replies
761
views
News:
Bioconductor's Transition Away from Twitter/X
Bioconductor
2.1 years ago
Maria Doyle
▴ 110
0
votes
1
reply
1.8k
views
sampling random regions of same nucleotide composition from hg38 genome
annotatr
regioneR
gkmSVM
updated 2.1 years ago by
Mahmoud
• 0 • written 5.0 years ago by
rohitsatyam102
▴ 20
0
votes
10
replies
2.0k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
2.1 years ago • updated 22 months ago
ScafioRuo
• 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
2.1 years ago
jared.andrews07
▴ 30
0
votes
1
reply
673
views
gene aligning reference
geneRecommender
gene
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Gülsüm
• 0
0
votes
0
replies
635
views
accesing gene name RNAseq
genetics
GeneticsPed
Genetics
2.1 years ago
Gülsüm
• 0
3
votes
5
replies
2.4k
views
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
sesame
IlluminaHumanMethylationEPICv2anno.20a1.hg38
methylationEPICv2.0
EpicV2
updated 21 months ago by
aldea85
• 0 • written 2.2 years ago by
Courtney
▴ 10
2
votes
4
replies
1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
2.1 years ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
602
views
DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
ari.bo
• 0
0
votes
0
replies
738
views
Identifying populations within a FlowSOM tree
FlowSOM
2.1 years ago
agus_rizzo
• 0
1
vote
2
replies
3.3k
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
948
views
Sign Output Values PADOG
PADOG
written 2.1 years ago by
tim.meese
• 0
0
votes
1
reply
702
views
EGSEA with Affymetrix data
EGSEA
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
cverschoor
• 0
3
votes
6
replies
1.7k
views
Methylation data analysis
MethylationArrayData
methylationArrayAnalysis
2.1 years ago
aldea85
• 0
0
votes
2
replies
1.6k
views
annotatePeak error for some problem
ChIPseeker
written 2.1 years ago by
Jones
• 0
0
votes
1
reply
697
views
COTAN mantainance
BuildReport
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Silvia
• 0
0
votes
0
replies
1.6k
views
Version map cannot be validated - not mapping to new bioconductor website
Install
2.1 years ago
Alexander
• 0
0
votes
0
replies
732
views
News:
CRAN downtime
BiocManager
Bioconductor
2.2 years ago
shepherl
4.2k
0
votes
0
replies
504
views
R/sql code to find the haplotype data from patient's rsIDs
starallele
phenoTest
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
greeshmathulasi1
• 0
0
votes
2
replies
1.4k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome
DESeq2
2.2 years ago • updated 2.1 years ago
anton.kratz
▴ 60
46,709 results • Page
38 of 935
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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