1
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9
replies
7.7k
views
Installing Bioconductor packages in Docker
Bioconductor DOCKER RShiny
updated 14 months ago by • 0 • written 4.9 years ago by • 0
1
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2
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812
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Limma help (creating design matrix)
limma
4.9 years ago d808bc07 • 0
0
votes
9
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4.6k
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Rhdf5lib installation problem
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updated 4.9 years ago by ★ 6.6k • written 4.9 years ago by ▴ 160
1
vote
3
replies
2.9k
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Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
votes
1
reply
2.5k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 4.9 years ago by ▴ 20 • written 12.8 years ago by ▴ 340
3
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2
replies
2.9k
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Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.9 years ago Benjamin ▴ 20
2
votes
2
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1.4k
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Biocthis GHA recently fails for macOS
biocthis
4.9 years ago jeroen.gilis ▴ 100
0
votes
11
replies
3.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
0
votes
6
replies
2.1k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.9 years ago Ray ▴ 20
0
votes
0
replies
1.8k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.9 years ago jol.espinoz ▴ 40
2
votes
3
replies
1.6k
views
How to set aspect ratio and symmetric colour map in iSEE panels?
iSEE
updated 4.9 years ago by ▴ 350 • written 4.9 years ago by ▴ 70
2
votes
1
reply
2.3k
views
Issue with TxDb.Mmusculus.UCSC.mm10.knownGene "TXNAME" no longer UCSC style but ENSEMBL
TxDb.Mmusculus.UCSC.mm10.knownGene
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
8
replies
2.3k
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Error in running Combat function
sva ComBat
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 10
6
votes
9
replies
3.2k
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How to better design a Volcano plot
EnhancedVolcano
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 20
2
votes
2
replies
1.4k
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how to use biocParallel for large local variables?
BiocParallel
4.9 years ago oyoung122 ▴ 20
1
vote
2
replies
1.7k
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Incomplete GWAS Catalog Data from makeCurrentGwascat()
gwascat r
4.9 years ago anailis • 0
0
votes
1
reply
671
views
Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
6
votes
6
replies
2.4k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.9 years ago MoltenLight ▴ 10
1
vote
1
reply
1.1k
views
Understanding proActiv promoter identification
proActiv
updated 4.9 years ago by ▴ 60 • written 4.9 years ago by ▴ 10
1
vote
3
replies
1.7k
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Error by installing BiocManager
BiocInstaller BiocManager Bioconductor
4.9 years ago adklts • 0
0
votes
3
replies
1.9k
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Does DiffBind correctly designate peaks with very small fold-change to be statistically significant?
DESeq2 DiffBind
updated 4.6 years ago by ★ 5.2k • written 4.9 years ago by ▴ 10
1
vote
3
replies
1.4k
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Question regarding lib.sizes when using glmQLFit
glmQLFit edgeR
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 170
0
votes
2
replies
1.3k
views
I am getting a segfault reading a SBML file with rsbml_read
rsbml
4.9 years ago Robert Dunne ▴ 10
0
votes
0
replies
1.3k
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Job: Scientist/Senior Scientist, Statistical Geneticist
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4.9 years ago António Miguel de Jesus Domingues ▴ 510
3
votes
3
replies
2.1k
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first error: could not find function "readGAlignments" in BiocParallel
BiocParallel
4.9 years ago Guandong Shang ▴ 40
1
vote
1
reply
1.6k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
3
replies
2.0k
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topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
6
replies
2.7k
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Is there any guide for analyzing HTA (Human Transcriptome Array 2.0) microarrays?
hta20probeset.db
4.9 years ago • updated 3.0 years ago komes42112 • 0
3
votes
11
replies
4.5k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 3.4 years ago by • 0 • written 4.9 years ago by ▴ 20
0
votes
3
replies
1.5k
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Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.9 years ago zefrieira • 0
1
vote
2
replies
4.5k
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Error while Installing BSgenome.Hsapiens.UCSC.hg38
BSgenome.Hsapiens.UCSC.hg38
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 20
1
vote
1
reply
1.1k
views
What is the correct interpretation of the p-value in GreyListChIP?
GreyListChIP
updated 4.9 years ago by ▴ 670 • written 4.9 years ago by ▴ 10
1
vote
3
replies
6.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.9 years ago by • 0
2
votes
4
replies
7.2k
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Complexheatmap Installation Issue
ComplexHeatmap
4.9 years ago legro.melanie • 0
4
votes
2
replies
2.3k
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ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
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updated 4.9 years ago by ★ 2.1k • written 4.9 years ago by • 0
1
vote
1
reply
1.5k
views
DEseq2 complex design - 2 factors with more than 2 levels
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
1
vote
8
replies
3.5k
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DiffBind 'mc.cores' > 1 is not supported on Windows
DiffBind
4.9 years ago GM ▴ 10
0
votes
0
replies
1.2k
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Job: Computational biology of cancer (Postdoc Position)
JobPosting Basel Switzerland
4.9 years ago Robert Ivanek ▴ 750
1
vote
11
replies
3.6k
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Using the correct counts with lm function linear model
lm DESeq2
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 50
3
votes
5
replies
1.5k
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Validation of DESeq2 v1.30 results
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
vote
3
replies
2.6k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 10
0
votes
0
replies
1.2k
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DeqMS, too manny missing values in one condition
DEqMS
updated 4.9 years ago by 1.6k • written 4.9 years ago by • 0
0
votes
1
reply
1.2k
views
Error in "generateNull" with only one set of gene list
singscore generateNull
updated 4.9 years ago by • 0 • written 5.7 years ago by • 0
1
vote
2
replies
1.5k
views
How to load the new dataset and gene-sets into singscore package in R
software error
updated 4.9 years ago by • 0 • written 6.1 years ago by • 0
0
votes
1
reply
1.3k
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
5
votes
7
replies
3.9k
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Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
6
votes
6
replies
8.2k
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Checking/updating package versions
DiffBind
4.9 years ago bertb • 0
4
votes
5
replies
3.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 680
1
vote
4
replies
1.3k
views
why does this message board think my posts are in unsupported languages?
rsbml
4.9 years ago Robert Dunne ▴ 10
0
votes
3
replies
930
views
Strange patterns in Log2fold change output
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
46,694 results • Page 139 of 934
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
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
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