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9
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879
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How long does it usually take to complete dream() from start to finish?
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9 months ago hayleyw • 0
1
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4
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765
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MDS plot edgeR
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updated 8 months ago by 50k • written 8 months ago by ▴ 10
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4
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flowStats Search Error
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3
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Sign Output Values PADOG
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updated 6 months ago by • 0 • written 6 months ago by • 0
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Diffbind "No genome detected"
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updated 5 months ago by 66k • written 11 months ago by • 0
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2
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354
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Impute does not work
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12 weeks ago Laura • 0
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18
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Install DESeq2 problem for macbook pro M1 Max
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updated 5 months ago by • 0 • written 2.3 years ago by • 0
1
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3
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552
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Merging Methylation data (M-values) with phenotypic data
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updated 9 months ago by 66k • written 9 months ago by • 0
0
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2
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508
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EdgeR FTest
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updated 9 months ago by 50k • written 9 months ago by • 0
2
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5
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11k
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Conversion from counts to FPKM
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updated 7 months ago by • 0 • written 5.4 years ago by • 0
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2
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updated 10 months ago by 50k • written 10 months ago by • 0
1
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7
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enrichGOgradient color change
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updated 9 weeks ago by ★ 4.0k • written 6 months ago by • 0
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4
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Error using Bsmooth.tstat due to NAs
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updated 6 months ago by • 0 • written 9.7 years ago by ★ 13k
1
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3
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918
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
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updated 11 months ago by • 0 • written 12 months ago by • 0
1
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5
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608
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ChIPpeakAnno annotatePeakInBatch output
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6 months ago ilaria.maurizio • 0
3
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3
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371
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permutation test in edgeR
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9
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clarification about bumphunter value output
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updated 12 months ago by • 0 • written 6.2 years ago by • 0
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5
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DiffBind handling of replicates and consensus
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updated 7 months ago by ★ 5.2k • written 4.3 years ago by • 0
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Fail BiocManager::install(version='3.12')
BioManager
updated 9 weeks ago by ★ 4.1k • written 2.1 years ago by ▴ 20
0
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5
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985
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
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7 months ago dorota.komar • 0
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biomaRt server error, and mirrors do not help
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updated 7 months ago by • 0 • written 2.1 years ago by ▴ 40
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Differential expression analysis: Permutation Test
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updated 5 months ago by 50k • written 8.3 years ago by ▴ 90
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Installing Local packages in Bioconductor
package
updated 9 months ago by • 0 • written 2.0 years ago by • 0
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Getting rs ids using chr coordinates | Biomart
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updated 10 months ago by 66k • written 3.8 years ago by • 0
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written 2.7 years ago by ▴ 60
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11
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DESeq2 gene length normalisation
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updated 7 months ago by 42k • written 7 months ago by • 0
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4
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398
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limma with interaction term
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3 months ago • updated 12 weeks ago Jitendra ▴ 10
3
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8
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DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
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3
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7
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DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
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9 months ago casco ▴ 10
0
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2
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563
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 5 months ago by • 0
1
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3
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617
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Read Count Normalisation and validation of analysis
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2
votes
4
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Error EPICv2 ChAMP
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2
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2
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Remove duplicates of colData in TreeSummarizedExperiment
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updated 8 months ago by 42k • written 8 months ago by • 0
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Trouble Loading Data into Champ
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updated 11 months ago by • 0 • written 3.2 years ago by • 0
3
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11
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SD filtering before DEG analysis with limma : possible or not ?
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updated 11 months ago by 50k • written 11 months ago by • 0
2
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7
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975
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Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
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6 months ago kjngo ▴ 40
1
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2
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How to combine a bulk and pseudobulk dataset?
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2
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4
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DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
534
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SPIAT for HALO manual phenotype entry
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updated 9 months ago by • 0 • written 11 months ago by • 0
4
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9
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DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 9 months ago by ▴ 10 • written 9 months ago by ▴ 10
1
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2
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696
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unable to retrieve certain packages from bioconductor 3.15
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updated 9 months ago by 66k • written 9 months ago by ▴ 10
0
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5
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tximport all(file.exists(files)) is not TRUE
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updated 9 weeks ago by • 0 • written 7.7 years ago by • 0
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5
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How to use EnrichGo of Cluster Profiler
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written 3.3 years ago by • 0
6
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9
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updated 3 months ago by • 0 • written 3 months ago by • 0
1
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6
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527
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GSVA on separate healthy and disease datasets
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0
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4
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updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
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Need Help w/ Subset on GRangesList
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3 months ago mat149 ▴ 70
0
votes
2
replies
356
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Error in featureCounts matrix
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1
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3
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How does DESeq2 calculate FPKM values when gene lengths are not supplied?
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written 4.2 years ago by • 0
0
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DNAString: Standard checksum function?
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8.2 years ago • updated 17 days ago Henrik Bengtsson ★ 2.4k
1,747 results • Page 4 of 35
Recent ...
Replies
Comment: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.1k
Hi, What do you get if you run the following `httr::HEAD()` command? I noticed that you have `libcurl` version 8.3.0 from `curl::curl_vers…
Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you @mikelove for your patience and kind advice. So I assume the plots from R are valid. Best wishes.
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Votes
Comment: recount3 problem downloading data from source sra
Answer: Slightly different count plots from R and spreadsheet
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
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