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2
votes
1
reply
2.1k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData
Clustering
memory
SingleCellExperiment
edgeR
updated 16 months ago by
Aaron Lun
★ 29k • written 16 months ago by
Joseph
• 0
0
votes
0
replies
558
views
News:
Annual Nominations Open for CAB and TAB! Deadline Aug 31
TAB
CAB
Bioconductor
16 months ago
shepherl
4.2k
1
vote
2
replies
807
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
16 months ago • updated 15 months ago
DL
• 0
0
votes
3
replies
690
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace
cytocq
updated 16 months ago by
SamGG
▴ 360 • written 16 months ago by
anders.tondell
▴ 30
0
votes
1
reply
778
views
edgeR - design a complex matrix
design
model.matrix
edgeR
complexdesign
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Karla
• 0
1
vote
4
replies
1.5k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
16 months ago
kschecht
• 0
0
votes
1
reply
1.1k
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 16 months ago by
Axel Klenk
★ 1.1k • written 16 months ago by
Bioinformagician
• 0
0
votes
0
replies
559
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
Community
Conference
Bioconductor
EuroBioC2024
16 months ago
Maria Doyle
▴ 110
0
votes
1
reply
701
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData
CEMiTool
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Menna
• 0
3
votes
3
replies
1.1k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Ahdee
▴ 60
2
votes
3
replies
911
views
EBImage Rendering of a DelayedArray Object
DelayedArray
EBImage
cytomapper
updated 6 months ago by
Hervé Pagès
16k • written 16 months ago by
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.5k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub
AnnotationDbi
AnnotationForge
16 months ago
Anna
• 0
0
votes
3
replies
902
views
RNA-seq with DESeq2 shrinkage estimation
Regression
DESeq2
rnaseqGene
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
David W. H.
• 0
0
votes
4
replies
1.2k
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts
Subread
Bioconductor
16 months ago
Jessica
• 0
2
votes
8
replies
3.8k
views
biomaRt getLDS error
biomaRt
16 months ago
mark.dunning
▴ 20
1
vote
2
replies
864
views
Question on number of genes used in GO analysis
GO
clusterProfiler
16 months ago
Danté
• 0
6
votes
15
replies
2.5k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 16 months ago by
kubracelikbas4
• 0
0
votes
4
replies
977
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 16 months ago by
shepherl
4.2k • written 16 months ago by
Fang
• 0
0
votes
4
replies
1.3k
views
WTChimeraData() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out
WTChimeraData
MouseGastrulationData
WT
16 months ago
haidan
• 0
1
vote
2
replies
1.3k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
16 months ago
grothmn
• 0
4
votes
4
replies
1.7k
views
NAs in fgseaMultilevel
fgsea
updated 16 months ago by
alserg
▴ 280 • written 16 months ago by
Danté
• 0
1
vote
2
replies
911
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts
Rsubread
16 months ago
Anke
• 0
0
votes
8
replies
1.4k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 16 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
Marianna
▴ 20
1
vote
1
reply
1.0k
views
biomaRt getSequence(): Error in .lock2
ensembldb
getSequence
updated 16 months ago by
Mike Smith
★ 6.6k • written 16 months ago by
Melanie
▴ 10
0
votes
2
replies
1.8k
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
updated 5 months ago by
juansmurphy
• 0 • written 16 months ago by
hayleyw
• 0
0
votes
5
replies
1.1k
views
preprocessENmix colnames Error
ENmix
Preprocessing
16 months ago
Eve
• 0
0
votes
1
reply
1.2k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2
LRT
Wald
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Eric
• 0
4
votes
7
replies
2.2k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
updated 16 months ago by
jessica.anderson
▴ 10 • written 17 months ago by
BioinfGuru
▴ 70
2
votes
4
replies
1.2k
views
how limma work with continous variables
GordonSmyth
limmaGUI
lmFit
voom
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
adR
▴ 40
0
votes
1
reply
845
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
updated 16 months ago by
Michael Love
43k • written 16 months ago by
smac_head
• 0
0
votes
1
reply
972
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
updated 16 months ago by
Michael Love
43k • written 16 months ago by
Eric
• 0
0
votes
1
reply
691
views
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH
SpatialExperiment
16 months ago
Matthew Thornton
▴ 390
5
votes
7
replies
3.2k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws
AnnotationDbi
written 17 months ago by
georgii.vdovin
• 0
2
votes
3
replies
1.0k
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 22 months ago by
tamivico
• 0
0
votes
2
replies
1.1k
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 8 months ago by
Rohit
• 0 • written 16 months ago by
nhaus
▴ 70
2
votes
3
replies
3.0k
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
written 16 months ago by
robledoj13
• 0
1
vote
0
replies
899
views
News:
Bioconductor Package Download Rate Limitation (HTTP 429)
downloads
http429
http
Bioconductor
16 months ago
shepherl
4.2k
0
votes
3
replies
1.9k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 16 months ago by
Maryna
• 0 • written 2.2 years ago by
Michael
• 0
0
votes
0
replies
602
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
16 months ago
louis.der.hammer
• 0
0
votes
9
replies
2.2k
views
'path' must be string
HELP
path
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
cpierce2
• 0
0
votes
4
replies
1.3k
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 16 months ago by
ATpoint
★ 5.0k • written 2.5 years ago by
seline.natalie
• 0
3
votes
6
replies
1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 16 months ago by
MedocRafael
• 0
4
votes
3
replies
1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
written 16 months ago by
mila
▴ 10
0
votes
0
replies
647
views
Error in serialization
scDblFinder
BiocParallel
16 months ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
743
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 16 months ago by
shepherl
4.2k • written 16 months ago by
Sadman
• 0
4
votes
12
replies
5.8k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 16 months ago by
Tim Peters
▴ 230 • written 2.0 years ago by
rae.alshammari
▴ 20
0
votes
3
replies
938
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
16 months ago
gallantk5
• 0
0
votes
3
replies
996
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 16 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Mark
• 0
1
vote
1
reply
1.2k
views
Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 16 months ago by
Matt Eldridge
▴ 10 • written 16 months ago by
Giulia
• 0
0
votes
0
replies
659
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
16 months ago
ramiro.barrantes
▴ 10
46,689 results • Page
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Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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