4
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9
replies
288
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
3
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2
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690
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Does this RNAseq experiment require a repeated measures approach?
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updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
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1
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1.5k
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Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by 66k • written 9 months ago by ▴ 10
3
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4
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700
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Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
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updated 10 months ago by 66k • written 10 months ago by • 0
3
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3
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732
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EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
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3
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254
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
3
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2
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1.1k
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ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
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updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
3
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1
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1.9k
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TwoSampleMR and ieugwasr
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updated 9 weeks ago by ▴ 10 • written 2.2 years ago by ▴ 90
3
votes
2
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456
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biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
6 months ago • updated 5 months ago henrydionne ▴ 10
3
votes
5
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673
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DESEQ Inquiry
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updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
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5
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Error: 'IdClusters'
DECIPHER
updated 12 months ago by ▴ 10 • written 15 months ago by • 0
3
votes
2
replies
590
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tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 66k • written 5 months ago by • 0
3
votes
4
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913
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DMRcate design
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8 months ago • updated 7 months ago Jitendra ▴ 10
3
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4
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Protein differential Expression analysis
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updated 9 months ago by ★ 4.1k • written 6.4 years ago by • 0
3
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4
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Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
3
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3
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13k
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How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by • 0 • written 5.3 years ago by • 0
3
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4
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1.3k
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Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
votes
16
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2.2k
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DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 4 months ago by 3.9k • written 2.9 years ago by ▴ 10
3
votes
6
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1.0k
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Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
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10 months ago abhisek001 • 0
3
votes
3
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9.6k
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How to find rsID with biomaRt in R
biomaRt
updated 3 months ago by 66k • written 3.2 years ago by ▴ 10
3
votes
1
reply
156
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How to save the DEXSeq results
DEXSeq
updated 15 days ago by 42k • written 15 days ago by • 0
3
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7
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5.5k
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error with champ.load
champ
written 6.6 years ago by ▴ 10
3
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8
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571
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Downloading package mixOmics
mixOmics
12 weeks ago noortje_bloem94 • 0
3
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3
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596
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comparing contrasts in edger/lima using makeContrasts function
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updated 8 months ago by 66k • written 8 months ago by • 0
3
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4
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565
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
6 months ago • updated 5 months ago pl23 • 0
3
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5
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2.2k
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Why the LogFC and delta-beta value are different in ChAMP
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3
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16
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18k
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featureCounts - paired-end data
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updated 11 months ago by • 0 • written 9.0 years ago by ▴ 140
3
votes
4
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531
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Right way to pseudobulk donors across replicates in edgeR
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updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 50
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.1 years ago by ▴ 60
3
votes
3
replies
275
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
3
votes
8
replies
937
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DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
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written 6 months ago by ▴ 10
3
votes
6
replies
863
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
11
replies
5.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 3 months ago by ★ 4.0k • written 3.3 years ago by • 0
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votes
4
replies
297
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Store output of matchPWM()
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20 days ago • updated 7 days ago mat149 ▴ 70
3
votes
1
reply
444
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NPARC package y-variable
NPARC NPA
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
3
votes
2
replies
240
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
8 weeks ago Anita ▴ 10
3
votes
1
reply
344
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News: Bioconductor.org has a new look!
Bioconductor Website
written 4 months ago by 3.9k
3
votes
6
replies
2.2k
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Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 66k • written 19 months ago by ▴ 10
3
votes
1
reply
329
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 40
3
votes
3
replies
459
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 8 weeks ago by ▴ 160 • written 8 weeks ago by • 0
3
votes
4
replies
270
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Help with error using camera() in limma
CAMERA limma
21 days ago • updated 20 days ago Chris ▴ 10
3
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5
replies
307
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Help with running egsea()
EGSEA
14 days ago • updated 13 days ago Chris ▴ 10
3
votes
1
reply
772
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News: [Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv spatialLIBD News
written 4.2 years ago by ★ 1.0k
3
votes
1
reply
1.5k
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Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job Job machine learning deep learning computational biology
written 6.4 years ago by ▴ 180
3
votes
6
replies
2.8k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 12 weeks ago by • 0 • written 5.3 years ago by ▴ 50
3
votes
3
replies
426
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
3
votes
3
replies
4.8k
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Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 11 months ago by ★ 4.0k • written 4.1 years ago by • 0
3
votes
2
replies
405
views
cant' download fgsea_1.20.0.tar.gz
download fgsea
9 months ago luca.s ▴ 50
3
votes
5
replies
1.2k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor Install library biocmanager
updated 10 months ago by 6.7k • written 10 months ago by ▴ 20
3
votes
5
replies
1.4k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1,748 results • Page 4 of 35
Recent ...
Replies
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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