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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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^.*\.Rproj$
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^\.Rproj\.user$

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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inst/doc

‎CaSpER.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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PackageRoxygenize: rd,collate,namespace,vignette

‎DESCRIPTION

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Package: CaSpER
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Type: Package
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Title: Identify large-scale CNV events from single cell or bulk RNA-Seq data
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Version: 0.1.0
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Author: Akdes Serin Harmanci, Arif O. Harmanci
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Maintainer: Akdes Serin Harmanci <[email protected]>
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Description: More about what it does (maybe more than one line)
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Use four spaces when indenting paragraphs within the Description.
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License:
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Encoding: UTF-8
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LazyData: true
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LinkingTo: Rcpp
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Depends: Rcpp, signal, pheatmap, RColorBrewer, HMMcopy, IRanges, grid, GenomeGraphs, ggplot2, reshape, mclust, ggpubr, scales, gridExtra, igraph, intergraph, ggnetwork, philentropy, ape, biomaRt, limma, GO.db, org.Hs.eg.db, GOstats
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RoxygenNote: 6.0.1
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Suggests: knitr,
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rmarkdown
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VignetteBuilder: knitr
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Package: CaSpER
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Type: Package
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Title: Identify large-scale CNV events from single cell or bulk RNA-Seq data
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Version: 0.1.0
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Author: Akdes Serin Harmanci, Arif O. Harmanci
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Maintainer: Akdes Serin Harmanci <[email protected]>
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Description: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data
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Encoding: UTF-8
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LazyData: true
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LinkingTo: Rcpp
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Depends: Rcpp, signal, pheatmap, RColorBrewer, HMMcopy, IRanges, grid, GenomeGraphs, ggplot2, reshape, mclust, ggpubr, scales, gridExtra, igraph, intergraph, ggnetwork, philentropy, ape, biomaRt, limma, GO.db, org.Hs.eg.db, GOstats
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RoxygenNote: 6.1.1
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Suggests: knitr,
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rmarkdown
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VignetteBuilder: knitr

‎NAMESPACE

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export(CreateCasperObject)
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export(lohCallMedianFilterByChr)
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export(lohCallMedianFilter)
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export(processMedianFiltering)
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export(ProcessData)
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export(PerformMedianFilter)
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export(PerformMedianFilterByChr)
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export(CenterSmooth)
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export(generateAnnotation)
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export(getDiffExprGenes)
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export(generateEnrichmentSummary)
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export(go.enrichment.BP)
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export(extractSegmentSummary)
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export(splitByOverlap)
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export(extractLargeScaleEvents)
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export(mergeScalesAndGenerateFinalEventSummary)
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export(goEnrichmentBP)
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export(gene.matrix)
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import(igraph)
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import(signal)
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import(pheatmap)

‎README.md

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Install dependencies first:
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``` r
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You may need to install libcurl-devel, libopenssl-devel and libxml2-devel
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ex: sudo yum -y install libxml2-devel.x86_64
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You may need to install libcurl-devel, libopenssl-devel openssl-devel and libxml2-devel
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ex: sudo yum -y install libxml2-devel libcurl-devel libopenssl-devel openssl-devel
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source("https://bioconductor.org/biocLite.R")
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biocLite(c('HMMcopy', 'GenomeGraphs', 'biomaRt', 'limma', 'GO.db', 'org.Hs.eg.db', 'GOstats'))
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1. [Yale meningioma Bulk RNA-Seq dataset](/demo/meningioma.R)
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2. [TCGA-GBM Bulk RNA-Seq dataset](/demo/tcga_GBM.R)
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3. [GBM Single-cell RNA-Seq dataset](/demo/sCellGBM.R)
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For running the examples, you can use Rscript command:
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Rscript /demo/meningioma.R
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Rscript /demo/tcga_GBM.R
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Rscript /demo/sCellGBM.R
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Each run generally takes about 5-20 minutes.

‎README.txt

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CaSpER
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---
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CaSpER is an algorithm for identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data.
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It takes as input:
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- Mapped RNA-Seq reads (Bam files)
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- Normalized expression matrix
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and outputs:
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- CNV events in multiscale resolution
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- Mutually exclusive and co-occurent CNV events
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Installation
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----------
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CaSpER is developed under R version 3.4.3.
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You can install CaSpER R package using the following R commands:
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Install dependencies first:
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You need to install libcurl-devel, libopenssl-devel, openssl-devel, and libxml2-devel
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>> sudo yum -y install libxml2-devel libcurl-devel libopenssl-devel openssl-devel
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Next it is necessary to install R package dependencies
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>> source("https://bioconductor.org/biocLite.R")
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>> biocLite(c('HMMcopy', 'GenomeGraphs', 'biomaRt', 'limma', 'GO.db', 'org.Hs.eg.db', 'GOstats'))
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Finally, to install CaSpER R package, use following:
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>> require(devtools)
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>> install_github("akdess/CaSpER")
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These commands are included in install_dependencies.sh and install_dependencies.R scripts.
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Please note that you may need to be root to install these dependencies.
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For extracting B-allele frequencies from RNA-Seq bam files download BAFExtract C++ source or binary code from https://github.com/akdess/BAFExtract.
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After downloading source code type the following:
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cd BAFExtract
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make clean
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make
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The executable is built under directory /bin.
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BAFExtract is developed and tested under CentOS 7.
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Usage
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----------
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Step 1. Merge single cell RNA-Seq bam files (required for single-cell studies)
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>> bamtools merge -list <bam_file_names> -out <sample_name>_merged.bam
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>> samtools index <sample_name>_merged.bam
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Step 2. Extract BAF values from RNA-Seq bam files
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>> samtools view <bam_file> | ./BAFExtract -generate_compressed_pileup_per_SAM stdin <genome_list> <sample_dir> 50 0; ./BAFExtract -get_SNVs_per_pileup <genome_list> <sample_dir> <genome_fasta_pileup_dir> 20 4 0.1 <output_baf_file>
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where
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<sample_dir>: the name of sample directory
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<output_baf_file>: final output
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You can download and unzip genome_fasta_pileup_dir files from :
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[for hg38](https://www.dropbox.com/s/ysrcfcnk7z8gyit/hg38.zip?dl=0)
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[for hg19](https://www.dropbox.com/s/a3u8f2f8ufm5wdj/hg19.zip?dl=0)
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You can download genome_list files from :
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[for hg38](https://www.dropbox.com/s/rq7v67tiou1qwwg/hg38.list?dl=0)
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[for hg19](https://www.dropbox.com/s/jcmt23nmuzm6poz/hg19.list?dl=0)
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Example run for BAFExtract:
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[download example rna-seq bam file](https://www.dropbox.com/s/1vl6iip0b8jwu66/SRR1295366.sorted.bam?dl=0)
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```{bash}
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mkdir test; samtools view SRR1295366.sorted.bam | ./bin/BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list test 50 0; ./bin/BAFExtract -get_SNVs_per_pileup hg38.list test ./hg38/ 20 4 0.1 test.baf
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```
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Step 3. Run CaSpER R package (See tutorials below)
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Tutorials
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----------
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1. [Yale meningioma Bulk RNA-Seq dataset](/demo/meningioma.R)
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2. [TCGA-GBM Bulk RNA-Seq dataset](/demo/tcga_GBM.R)
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3. [GBM Single-cell RNA-Seq dataset](/demo/sCellGBM.R)
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For running the examples, you can use Rscript command:
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Rscript /demo/meningioma.R
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Rscript /demo/tcga_GBM.R
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Rscript /demo/sCellGBM.R
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Each run generally takes about 5-20 minutes.

‎install_dependencies.R

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#source("https://bioconductor.org/biocLite.R")
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#biocLite(c('HMMcopy', 'GenomeGraphs', 'biomaRt', 'limma', 'GO.db', 'org.Hs.eg.db', 'GOstats'))
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install.packages('devtools');
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require(devtools)
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install_github("akdess/CaSpER")

‎install_dependencies.sh

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sudo yum -y install libcurl-devel libopenssl-devel libxml2-devel openssl-devel
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