0
votes
0
replies
563
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
16 months ago user_bioinfo • 0
0
votes
3
replies
1.1k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 16 months ago by • 0
3
votes
5
replies
2.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
2
votes
1
reply
1.6k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
0
votes
1
reply
637
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
16 months ago mdidish ▴ 10
0
votes
0
replies
539
views
DiffBind dba.plotprofile y-axis range
DiffBind
16 months ago Tara • 0
2
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4
replies
873
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Bioconductor Submission question
Bioconductor
16 months ago XFWu • 0
2
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3
replies
1.3k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
16 months ago BioinfGuru ▴ 70
2
votes
2
replies
897
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
16 months ago BioinfGuru ▴ 70
0
votes
0
replies
476
views
proActiv-promoter analysis
proActiv Transcriptomics
16 months ago wang.xiangyu • 0
2
votes
1
reply
2.2k
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
votes
0
replies
567
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
813
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
16 months ago DL • 0
0
votes
3
replies
721
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace cytocq
updated 16 months ago by ▴ 360 • written 16 months ago by ▴ 30
0
votes
1
reply
802
views
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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1.5k
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How to Query Only SNPs from the biomaRt Variation Database
biomaRt
16 months ago kschecht • 0
0
votes
1
reply
1.2k
views
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
votes
0
replies
570
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
Community Conference Bioconductor EuroBioC2024
16 months ago Maria Doyle ▴ 110
0
votes
1
reply
711
views
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
votes
3
replies
1.1k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 16 months ago by 68k • written 16 months ago by ▴ 60
2
votes
3
replies
934
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EBImage Rendering of a DelayedArray Object
DelayedArray EBImage cytomapper
updated 7 months ago by 16k • written 16 months ago by ★ 1.6k
0
votes
3
replies
1.6k
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makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
16 months ago Anna • 0
0
votes
3
replies
918
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
4
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1.2k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
17 months ago • updated 16 months ago Jessica • 0
2
votes
8
replies
3.8k
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biomaRt getLDS error
biomaRt
16 months ago mark.dunning ▴ 20
1
vote
2
replies
881
views
Question on number of genes used in GO analysis
GO clusterProfiler
16 months ago Danté • 0
6
votes
15
replies
2.6k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
0
votes
4
replies
1000
views
Failed to install geneLenDataBase
geneLenDataBase ChAMP
updated 16 months ago by 4.2k • written 16 months ago by • 0
0
votes
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
replies
1.4k
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
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1.8k
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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
replies
940
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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
votes
8
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1.4k
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DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 16 months ago by ★ 5.2k • written 16 months ago by ▴ 20
1
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1
reply
1.1k
views
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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save.rnb.set warnings when trying to save rnb.set
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updated 6 months ago by • 0 • written 17 months ago by • 0
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5
replies
1.2k
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preprocessENmix colnames Error
ENmix Preprocessing
16 months ago Eve • 0
0
votes
1
reply
1.3k
views
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
votes
7
replies
2.3k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 16 months ago by ▴ 10 • written 17 months ago by ▴ 70
2
votes
4
replies
1.2k
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how limma work with continous variables
GordonSmyth limmaGUI lmFit voom
updated 16 months ago by 53k • written 16 months ago by ▴ 40
0
votes
1
reply
868
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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 17 months ago by • 0
0
votes
1
reply
983
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 16 months ago by 43k • written 17 months ago by • 0
0
votes
1
reply
706
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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 • 0
2
votes
3
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views
Comparing one group against multiple groups in DESeq2
DESeq2
written 23 months ago by • 0
0
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2
replies
1.1k
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 8 months ago by • 0 • written 17 months ago by ▴ 70
2
votes
3
replies
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Plot PCA with ellipses using ggplot
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written 17 months ago by • 0
1
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0
replies
913
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News: Bioconductor Package Download Rate Limitation (HTTP 429)
downloads http429 http Bioconductor
17 months ago shepherl 4.2k
0
votes
3
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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 17 months ago by • 0 • written 2.3 years ago by • 0
0
votes
0
replies
614
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
17 months ago louis.der.hammer • 0
0
votes
9
replies
2.2k
views
'path' must be string
HELP path
updated 17 months ago by 68k • written 17 months ago by • 0
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Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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C: DESeq2 Following RSEM
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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