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CHARM qcReport Question
charm charm
10.9 years ago zeynep özkeserli ▴ 160
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working with genome-wide phastCons scores
BSgenome convert BSgenome rtracklayer IRanges charm BSgenome convert BSgenome rtracklayer
11.4 years ago Robert Castelo ★ 3.4k
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Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
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updated 11.5 years ago by ▴ 50 • written 11.5 years ago by ★ 4.3k
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Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm
11.6 years ago Nitesh Turaga ▴ 50
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Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm
updated 11.6 years ago by ★ 4.3k • written 11.6 years ago by ▴ 50
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ShortRead 3' trimming negative length vectors are not allowed
charm charm
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 300
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Charm Error - methp
charm charm
11.8 years ago zeynep özkeserli ▴ 160
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1.9k
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Conversion of minfi format MethylSet to methyAnalysis format MethyGenoSet
Cancer charm minfi methyAnalysis Cancer charm minfi methyAnalysis
12.1 years ago Ed Schwalbe ▴ 20
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CHARM: Affymetrix 1.0R tiling arrays import
BSgenome affy BSgenome oligo charm BSgenome affy BSgenome oligo charm
12.1 years ago Guest User ★ 13k
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RCytoscape on Windows
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12.3 years ago Paul Shannon ▴ 750
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[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
12.3 years ago Kasper Daniel Hansen ★ 6.5k
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CHARM - The following columns in sampleKey...
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updated 12.4 years ago by ▴ 120 • written 12.4 years ago by ★ 13k
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Question about interpretation of CHARM results
charm charm
updated 12.6 years ago by ▴ 120 • written 12.6 years ago by ▴ 160
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Scripts for CHARM data analysis
charm charm
updated 12.6 years ago by ★ 4.2k • written 12.6 years ago by ▴ 10
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How can I identify the closest transcript from a chromosome coordinate?
Microarray Genetics probe charm Microarray Genetics probe charm
12.7 years ago Yoo, Seungyeul ▴ 110
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4
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2.0k
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How can I obtain gene name from chromosome location?
Lung charm genomes Lung charm genomes
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ▴ 110
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error in dmrFinder of charm package when there is one sample per group
charm charm
12.7 years ago P. Murakami ▴ 30
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908
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error in dmrFinder of charm package when there is one sample per group
charm charm
12.7 years ago Tarca, Adi ▴ 570
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989
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charm package using MEDIP protocol
charm charm
12.8 years ago Tarca, Adi ▴ 570
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1.5k
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Nimblegen promoter medip array platform design file problem
BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation
12.9 years ago zeynep özkeserli ▴ 160
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1.5k
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Nimblegen promoter medip array platform design file problem
BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation
12.9 years ago zeynep özkeserli ▴ 160
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752
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GOHyperGResult in a data.frame, possible NAMESPACE problem?
charm charm
15.2 years ago Robert Castelo ★ 3.4k
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1.2k
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biomaRt proxy issues
GO biomaRt charm GO biomaRt charm
16.0 years ago Steve Pederson ▴ 60
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1.0k
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Problems reading multiple MAQ map files with ShortRead ReadAligned
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16.0 years ago David Rossell ▴ 100
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1
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1.1k
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Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
16.0 years ago Martin Morgan 25k
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Assistant/Associate Professor Department of Biostatistics
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16.0 years ago Kellie J. Archer, Ph.D. ▴ 120
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2
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5.7k
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biomaRt proxy issues
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updated 16.1 years ago by ▴ 600 • written 16.1 years ago by ▴ 60
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Problem with Rgraphviz on OSX with libgvc
graph Rgraphviz charm graph Rgraphviz charm
updated 18.2 years ago by ★ 7.4k • written 18.2 years ago by ▴ 80
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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