2
votes
1
reply
2.1k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 16 months ago by ★ 29k • written 16 months ago by • 0
0
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0
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558
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News: Annual Nominations Open for CAB and TAB! Deadline Aug 31
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16 months ago shepherl 4.2k
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2
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807
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
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16 months ago • updated 15 months ago DL • 0
0
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3
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690
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How to combine multiple lists of cytoframes/cytocq data objects into one
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updated 16 months ago by ▴ 360 • written 16 months ago by ▴ 30
0
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1
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778
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 16 months ago by 53k • written 16 months ago by • 0
1
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4
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How to Query Only SNPs from the biomaRt Variation Database
biomaRt
16 months ago kschecht • 0
0
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1
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1.1k
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Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 16 months ago by ★ 1.1k • written 16 months ago by • 0
0
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0
replies
559
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EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
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16 months ago Maria Doyle ▴ 110
0
votes
1
reply
701
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 16 months ago by 68k • written 16 months ago by • 0
3
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3
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1.1k
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 16 months ago by 68k • written 16 months ago by ▴ 60
2
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3
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911
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EBImage Rendering of a DelayedArray Object
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updated 6 months ago by 16k • written 16 months ago by ★ 1.6k
0
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3
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1.5k
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makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
16 months ago Anna • 0
0
votes
3
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902
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RNA-seq with DESeq2 shrinkage estimation
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updated 16 months ago by 68k • written 16 months ago by • 0
0
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4
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1.2k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
16 months ago Jessica • 0
2
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8
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3.8k
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biomaRt getLDS error
biomaRt
16 months ago mark.dunning ▴ 20
1
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2
replies
864
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Question on number of genes used in GO analysis
GO clusterProfiler
16 months ago Danté • 0
6
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15
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2.5k
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Deseq2 design formula and analysis with internal controls
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updated 15 months ago by ★ 1.4k • written 16 months ago by • 0
0
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4
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977
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Failed to install geneLenDataBase
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updated 16 months ago by 4.2k • written 16 months ago by • 0
0
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4
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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
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2
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1.3k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
16 months ago grothmn • 0
4
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4
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1.7k
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NAs in fgseaMultilevel
fgsea
updated 16 months ago by ▴ 280 • written 16 months ago by • 0
1
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2
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911
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
16 months ago Anke • 0
0
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8
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1.4k
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DiffBind full library size not reliable
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updated 16 months ago by ★ 5.2k • written 16 months ago by ▴ 20
1
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1
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1.0k
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biomaRt getSequence(): Error in .lock2
ensembldb getSequence
updated 16 months ago by ★ 6.6k • written 16 months ago by ▴ 10
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2
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1.8k
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
updated 5 months ago by • 0 • written 16 months ago by • 0
0
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5
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1.1k
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preprocessENmix colnames Error
ENmix Preprocessing
16 months ago Eve • 0
0
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1
reply
1.2k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 16 months ago by 68k • written 16 months ago by • 0
4
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7
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2.2k
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What does evidence of batch effect in bulk rnaseq look like?
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updated 16 months ago by ▴ 10 • written 17 months ago by ▴ 70
2
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4
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1.2k
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how limma work with continous variables
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updated 16 months ago by 53k • written 16 months ago by ▴ 40
0
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1
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845
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 16 months ago by 43k • written 16 months ago by • 0
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972
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
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updated 16 months ago by 43k • written 16 months ago by • 0
0
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1
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691
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Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
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16 months ago Matthew Thornton ▴ 390
5
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7
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Mapping Between GenBank ID's and Uniprot
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Comparing one group against multiple groups in DESeq2
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2
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Validity of SingleR with very small bulk RNAseq reference
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2
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3
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Plot PCA with ellipses using ggplot
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written 16 months ago by • 0
1
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0
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899
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16 months ago shepherl 4.2k
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3
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How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
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updated 16 months ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
602
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Sigmatrix should not contain missing values error in deconvolution using granule
granulator
16 months ago louis.der.hammer • 0
0
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9
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2.2k
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'path' must be string
HELP path
updated 16 months ago by 68k • written 16 months ago by • 0
0
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4
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1.3k
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Recount3: PCR duplicates
pcrduplicates recount3 multimappingreads
updated 16 months ago by ★ 5.0k • written 2.5 years ago by • 0
3
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6
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1.3k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 16 months ago by • 0
4
votes
3
replies
1.6k
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
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written 16 months ago by ▴ 10
0
votes
0
replies
647
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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 4.2k • written 16 months ago by • 0
4
votes
12
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5.8k
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How to get DMR for Infinium methylation EPIC v2
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updated 16 months ago by ▴ 230 • written 2.0 years ago by ▴ 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 ★ 5.0k • written 16 months ago by • 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 ▴ 10 • written 16 months ago by • 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 18 of 934
Recent ...
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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
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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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