├── DESCRIPTION ├── NAMESPACE ├── R ├── MismatchFinder.R ├── ScisorWiz_2File.R └── ScisorWiz_AllInfo.R ├── README.Rmd ├── README.Rmd~ ├── README.md ├── README.md~ ├── inst ├── RScript │ ├── PlotIsoforms.r │ └── interactivePlot.R ├── doc │ ├── ScisorWiz-vignette.R │ ├── ScisorWiz-vignette.Rmd │ └── ScisorWiz-vignette.pdf ├── extdata │ ├── Snap25.mismatches.txt.gz │ ├── gencode.vM21.annotation.gtf.gz │ └── userInput │ │ ├── AllInfo │ │ ├── AllInfo.gz │ │ ├── barcode_cellType_assignments │ │ ├── cellTypeFile_Snap25.tab │ │ ├── fqFolder │ │ ├── P7HIPP_subset.fastq.gz │ │ ├── sorted.Snap25.bam │ │ └── sorted.Snap25.bam.bai │ │ ├── readinfo.gff.gz │ │ └── readstogenes.genes.gz └── python │ ├── ClusterByIsoform_AllInfoInput.py │ ├── ClusterByIsoform_gffInput.py │ ├── mismatch_finder.py │ └── start_end_finder.py ├── man ├── MismatchFinder.Rd ├── ScisorWiz_2File.Rd ├── ScisorWiz_AllInfo.Rd └── figures │ ├── ScisorWiz_Workflow.png │ ├── Snap25_Isoform_Plot.pdf │ ├── Snap25_Isoform_Plot_noMis.pdf │ ├── Snap25_Isoform_Plot_testdata.pdf │ ├── Snap25_Isoform_Plot_testdata_2File_Mis.pdf │ ├── Snap25_Isoform_Plot_testdata_2File_NoMis.pdf │ ├── Snap25_Isoform_Plot_testdata_AllInfo.pdf │ ├── Snap25_Isoform_Plot_testdata_AllInfo_NoMis.pdf │ └── Snap25_Isoform_Plot_testdata_noMis.pdf └── vignettes ├── ScisorWiz-vignette.Rmd └── ScisorWiz-vignette.pdf /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ans4013/ScisorWiz/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ans4013/ScisorWiz/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/MismatchFinder.R: -------------------------------------------------------------------------------- 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