2
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4
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1.7k
views
Import a Bioconductor package that is only used in a vignette/.Rmd script
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updated 2.2 years ago by 4.3k • written 2.2 years ago by • 0
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4
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rnaSeqGene workflow not available in Bioconductor 3.18
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9
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6
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2
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MA plot for DESEq2 analysis
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0
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636
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SGSeq how export PSI values for each typr of splice variant
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1
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1
reply
625
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DESeqResults object -> extract statistics results with rownames (gene)
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updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 50
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3
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Support for installation and usage of TxDb.Hsapiens.UCSC.hg19.knownGene package in R version 4.2.2
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2.2 years ago blessybo • 0
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7
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Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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3
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929
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DESeq2: FPMs varying based on sample groups used
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4
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
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2.2 years ago Wending • 0
1
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1
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Deploying to shinyapps.io returns error for BiocVersion and phangorn packages
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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0
replies
901
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Gviz::GeneRegionTrack error with standard TxDb: "adding seqlevels to a TxDb object is not supported"
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2.2 years ago dbsgtk • 0
0
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8
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1.7k
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Quickly calculating adjusted Fold Change with DESeq2
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2.2 years ago Luca • 0
1
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0
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1.1k
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Gviz : UcscTrack
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2.2 years ago yujin ▴ 10
0
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7
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Unable to install RefPlus - R=4.3.1, BiocManager=3.18
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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1
reply
983
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.2 years ago NiKo ▴ 10
0
votes
6
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1.5k
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
0
replies
767
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Mfuzz package loading issues
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2.2 years ago Jon • 0
0
votes
1
reply
687
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Advice needed on package using online databases (fails CHECK when database is down)
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updated 2.2 years ago by 4.3k • written 2.2 years ago by ▴ 30
0
votes
0
replies
909
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
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2.2 years ago mch • 0
1
vote
3
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1.2k
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Error in Gviz (actually, rtracklayer) | IdeogramTrack
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updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 10
12
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10
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biomaRt not working - lazy table error
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4
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Mfuzz package loading issues
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2.2 years ago Jon • 0
0
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2
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885
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Can you help me generate a Bsgenome of the fusion genome of a human and HIV-1 virus?
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2.2 years ago 13273976287 • 0
0
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1
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Error when trying to create a heatmap with DESeq2
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6
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2
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DecideTest vs topTAGs in edgeR
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updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
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How to calculate CDS start and End per transcript from GTF file
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2.2 years ago rohitsatyam102 ▴ 20
2
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10
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Accounting for Batch effect reduces DEGs drastically
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2.2 years ago rohitsatyam102 ▴ 20
2
votes
9
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object HPOGENE is not exported by namespace HPO.db
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updated 2.2 years ago by ▴ 50 • written 2.2 years ago by ▴ 30
4
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10
replies
3.1k
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Archives prior to 3.15 gone
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updated 2.2 years ago by 4.3k • written 3.3 years ago by ▴ 30
0
votes
3
replies
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determine if R package or it's dependencies functionality require internet access
biomaRt
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
0
votes
2
replies
1.1k
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can't update bioconductor 3.18
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2.2 years ago feifan • 0
3
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4
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5
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6
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DESeq2 Normalization with 4 Groups
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1
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2
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0
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2
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How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
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0
replies
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error while running DMRcate
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votes
4
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How to correct for known and surrogate variables in DESeq2?
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votes
1
reply
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DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
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updated 2.3 years ago by 4.3k • written 2.3 years ago by • 0
0
votes
1
reply
1.7k
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Problems when running GDC_prepare in R
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2.3 years ago leon • 0
0
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5
replies
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Limma continuous design (association polygenic risk score with gene expression)
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updated 2.2 years ago by 53k • written 2.3 years ago by • 0
0
votes
1
reply
665
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MEDIPS - covariate
MEDIPS
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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1
reply
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Job: Job:Data Scientist / Bioinformatician / Statistician at University of California San Francisco (UCSF)
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2
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3
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.2 years ago by ★ 1.4k • written 2.3 years ago by • 0
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votes
4
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Need help generating BSgenome and orgdb
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2.3 years ago • updated 23 months ago mat149 ▴ 80
1
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1
reply
1.3k
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rtracklayer error for browserSession UCSC
rtracklayer
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 10
46,730 results • Page 40 of 935
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0
thank you very much. https://www.biostars.org/p/9617271/
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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