0
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2
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2.4k
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
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updated 8.8 years ago by 43k • written 8.8 years ago by • 0
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Boxplot for Raw Data
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updated 8.8 years ago by ▴ 20 • written 8.8 years ago by • 0
5
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1
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topGO under-representation table
topGO GO
8.9 years ago • updated 8.8 years ago beachboarder900 ▴ 40
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2
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Appropriate use of Limma Treat function
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
0
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2
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Using edgeR for small shRNA-seq screen analysis
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8.8 years ago sirintra ▴ 10
0
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2
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2.5k
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Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
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updated 8.8 years ago by 68k • written 8.8 years ago by • 0
0
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3
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2.5k
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Accessing the BigWig files from the web
rtracklayer
8.8 years ago Mustafa ABUELQUMSAN • 0
0
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1
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3.5 release schedule?
bioconductor
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by ▴ 470
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966
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virtualArray installation problem
R
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
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2
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does readVcf mistakenly ignore ploidy for missing genotypes?
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8.8 years ago TimothéeFlutre ▴ 80
0
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0
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2.0k
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Problem when using topGO for RNAseq data: The number of annotated genes for GO terms changes according to the number of genes in the gene-background-…
topGO gene ontolology rnaseq
8.8 years ago colaneri ▴ 30
9
votes
4
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4.4k
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GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
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updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
1
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4
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5.4k
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Transcript to gene in clariom d human affymetrix data
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8.8 years ago yahia.adnani • 0
1
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5
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1.6k
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Filter out ranges by number of probes
probe ranges
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by ▴ 30
0
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microarray data expression set
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8.8 years ago farahqureshi5 • 0
0
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0
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Has anyone used the RUV package for Microbiome data?
ruv
8.8 years ago sasha • 0
1
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6
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3.0k
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GoSeq SupportedGenomes error
goseq unsupported organisms supportedgenomes supportedorganisms error
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
2
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1
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1.1k
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Why export of empty GRanges to GFF fails?
rtracklayer
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 10
3
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1
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1.6k
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RNASeq testing for differential expression in one condition, equality in another (using DESeq)
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8.8 years ago ysdel ▴ 40
0
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1
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3.2k
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installation of Sleuth
devtools
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
0
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14
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Error through importing (project = 'SRP009615') or even to download any BigWig File
recount Tutorial
updated 8.8 years ago by ★ 1.1k • written 8.8 years ago by • 0
0
votes
5
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2.6k
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ChIPseq diffbind merging peaks
diffbind merging_peaks
8.8 years ago veronique.storme • 0
0
votes
1
reply
1.8k
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In ggbio, plot transcripts from a TxDb with gene labels
ggbio
updated 8.8 years ago by ★ 11k • written 8.8 years ago by • 0
0
votes
1
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1.8k
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Drawing a HeatMapList while retaining the original row order of each heat map
complexheatmap
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 150
0
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2
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1.2k
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Student at SJTU
limma
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
0
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0
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1.6k
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[oligo] Farms and DFW summalization of Affymetrix Clariom S array using oligo package
oligo farms
8.8 years ago snj • 0
1
vote
1
reply
2.0k
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Disease ontology in mouse and possible orthologue in human
bioconductor
updated 8.8 years ago by ★ 1.2k • written 9.2 years ago by • 0
3
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3
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1.5k
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limma decideTests: only p-value less than (but not equal to) alpha are flagged as significant
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updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 20
2
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2
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2.0k
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Can one get LSMeans and expression confidence intervals from limma and voom?
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8.8 years ago bag59 • 0
1
vote
10
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4.4k
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Issue creating a genomic state object in derfinder from an Ensembl GTF file
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8.8 years ago Leonardo Collado Torres ★ 1.1k
2
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3
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2.7k
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How to determine a set of empirical control 'genes' using RUVSeq
RUVSeq
updated 3.5 years ago by ▴ 30 • written 8.8 years ago by • 0
3
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2
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Job: Hunting for Human Infectious Agents in Cancer using data from Genomics England's 100,000 genome project : PhD Studentship @ UEA, Norwich
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8.8 years ago Daniel Brewer ▴ 100
3
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2
replies
2.0k
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How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by ▴ 30
4
votes
6
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2.1k
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Multi-factorial design for patient-replicates from different time points (Deseq2)
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updated 8.8 years ago by 43k • written 8.8 years ago by • 0
1
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3
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R-3.2.3 install package DESeq2 get wrong
deseq2
updated 8.8 years ago by ★ 1.5k • written 8.8 years ago by • 0
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3
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Question regarding best bioconductor package for RNA-seq
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updated 8.8 years ago by ▴ 370 • written 8.8 years ago by ▴ 10
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2
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flowCore compilatiopn issue with c++ library conflicting declarations
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8.8 years ago junk.yvert • 0
0
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1
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2.7k
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Error with DESeq2 installation
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updated 8.8 years ago by ▴ 40 • written 8.8 years ago by ▴ 10
0
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0
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1.3k
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cummeRbund error dealing with cuffdiff results
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8.8 years ago wastdc • 0
4
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7
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Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
papi metabolomics pathway analysis
updated 8.8 years ago by ▴ 10 • written 9.7 years ago by ▴ 10
4
votes
4
replies
3.2k
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ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
glmnet deseq2
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 40
1
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4
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4.2k
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clusterprofiler KEGG enrichment for arabidopsis
clusterprofiler
8.8 years ago chentong_biology ▴ 10
1
vote
1
reply
1.7k
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summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
bioconductor pdfinfobuilder microarray nimblegene oligo
8.8 years ago sorghills • 0
2
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4
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2.7k
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About Variance Stabilizing Transformation
deseq2
8.8 years ago panagiotis.mokos ▴ 40
2
votes
4
replies
1.8k
views
Ranges on AAStrings
AAString Views Biostrings
8.8 years ago tobias.kockmann ▴ 20
5
votes
3
replies
8.4k
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What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 40
0
votes
3
replies
1.4k
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IONiseR error when trying to call readFast5Summary on fast5 reads
IONiseR
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by • 0
1
vote
1
reply
1.5k
views
Correct for Gene Length bias in GO analysis of retrotransposition
GO gene ontology bias retrotransposition
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
3
votes
5
replies
2.6k
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How to find all available packages on BioConductor
bioconductor
8.8 years ago mick.jordan • 0
46,696 results • Page 345 of 934
Recent ...
Replies
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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