2
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2
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1.8k
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ExperimentHub full metadata
ExperimentHub
written 8 weeks ago by ▴ 50
1
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2
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Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
6 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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119
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
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updated 13 days ago by 43k • written 6 weeks ago by • 0
0
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1
reply
542
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cytolib uses outdated boost call
cytolib
updated 6 weeks ago by 68k • written 6 weeks ago by • 0
4
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8
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1.7k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
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6 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
2
replies
229
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can't post
devel
updated 6 weeks ago by 4.2k • written 6 weeks ago by • 0
7
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9
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5.3k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 weeks ago bbao ▴ 10
0
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1
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1.2k
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 6 weeks ago by 52k • written 16.6 years ago by ▴ 10
0
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2
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856
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Install old version of DESeq2
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updated 6 weeks ago by 68k • written 6 weeks ago by • 0
0
votes
1
reply
394
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 weeks ago by 68k • written 7 weeks ago by • 0
3
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1
reply
3.9k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 6 weeks ago by ★ 29k • written 7 weeks ago by ▴ 10
0
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0
replies
112
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Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace FlowCytometry
6 weeks ago Valeria • 0
0
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0
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129
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News: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
7 weeks ago Wei Shi ★ 3.6k
1
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3
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2.2k
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Regarding the issue of background genes in enrichment analysis
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written 7 weeks ago by ▴ 10
0
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3
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2.2k
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 7 weeks ago by 52k • written 8 weeks ago by • 0
2
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4
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3.1k
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I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis lncRNA
8 weeks ago John ▴ 10
0
votes
2
replies
863
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gene detection across experiments
DESeq2 Normalization
8 weeks ago Mara • 0
0
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3
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1.5k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 8 weeks ago by 68k • written 8 weeks ago by • 0
1
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3
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1.6k
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How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 3 months ago by • 0
5
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11
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 3 months ago by ▴ 10
1
vote
10
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6.1k
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 27 days ago by • 0 • written 2.4 years ago by ▴ 10
0
votes
5
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1.9k
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compute_fasta_digest does not match Salmon index hash
tximeta
written 5 months ago by • 0
0
votes
5
replies
683
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WGCNA
WGCNA Normalization RNASeq
written 6 months ago by • 0
3
votes
4
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5.0k
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Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 8 weeks ago by 68k • written 10 weeks ago by ▴ 10
0
votes
3
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1.0k
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TopGO question
topGO top
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
0
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2
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917
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Starting with a clean bioconductor rstudio container
Bioconductor
updated 9 weeks ago by ★ 4.9k • written 9 weeks ago by • 0
0
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1
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2.3k
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ChAMP pipeline error (champ.import)
software error
updated 9 weeks ago by • 0 • written 6.4 years ago by • 0
0
votes
2
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417
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 9 weeks ago by ★ 4.9k • written 9 weeks ago by • 0
1
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5
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3.5k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 4 weeks ago by 43k • written 11 weeks ago by • 0
0
votes
1
reply
603
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Which GTF file to use for creation of tx2gene files?
tximport
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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1
reply
2.0k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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1.1k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
0
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3
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838
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 8 weeks ago by • 0 • written 9 weeks ago by • 0
1
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2
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3.6k
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Is voomByGroup available in limma?
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10 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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4
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1.6k
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How to use goana function with zebrafish genome from org.Dr.eg.db
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10 weeks ago Eric • 0
1
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3
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1.2k
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News: Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt ensembldb
written 3 months ago by ▴ 30
0
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0
replies
25
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Spam: wealthdt5
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10 weeks ago Enfurry 0
0
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0
replies
186
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Y-axis break ihn Volcano Plot
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10 weeks ago rajdeepboral00 • 0
0
votes
0
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161
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getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC hcg110.db
updated 10 weeks ago by 4.2k • written 10 weeks ago by • 0
3
votes
2
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1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 11 weeks ago by ▴ 20
1
vote
2
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2.5k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 11 weeks ago by • 0
0
votes
0
replies
184
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Job: Job: Ensembl Dataflow Coordinator
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11 weeks ago Aleena_Ensembl ▴ 30
0
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1
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1.3k
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Retrieve Salmon transcript quantification file from recount3
recount3
updated 11 weeks ago by ★ 1.1k • written 12 weeks ago by ▴ 10
0
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1
reply
1.1k
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error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25 hcg110.db
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
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1
reply
826
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Source / binary version mismatch for rGADEM
rGADEM
updated 11 weeks ago by 4.2k • written 11 weeks ago by • 0
0
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9
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13k
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Bioconductor version cannot be validated
BiocManager Bioconductor
updated 11 weeks ago by • 0 • written 4.1 years ago by ▴ 10
3
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1
reply
3.7k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by ▴ 10
0
votes
2
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1.2k
views
Interaction in Design Experimental
rnaseqGene
12 weeks ago • updated 11 weeks ago Ferdinand David • 0
0
votes
0
replies
215
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Job: Lab Head positions at the WEHI, Melbourne, Australia
JobPosting Bioconductor
11 weeks ago Gordon Smyth 52k
1
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3
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2.0k
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Heatmap of the Count Matrix
rnaseqGene
updated 7 weeks ago by • 0 • written 12 weeks ago by • 0
46,608 results • Page 2 of 933
Recent ...
Replies
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do. I would personally check to see if there is any…
Comment: Can NanoString data be analyzed using DESeq2? by James W. MacDonald 68k
You can always discard, although you can also retain them to check for unexpected differences.
Comment: DESeq2 on NanoString Data by Michael Love 43k
Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc. It is close to SVA, we discuss both in the workflow…
Comment: DESeq2 on NanoString Data by thkapell ▴ 10
Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…
Comment: Can NanoString data be analyzed using DESeq2? by thkapell ▴ 10
Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…
Votes
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Comment: Are voomByGroup and voomLmFit compatible?
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