cnobles

iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

CART19_intsite_manuscript_analysis

Analysis provided in the "Linking outcome of CD19-directed CAR T-cell therapy with genome modification of vector integration" manuscript.

gintools

[Dev] Tools for genomic DNA integration analysis

blatCoupleR

[Depreciated, see nuckit repo] Join paired-end sequence alignments from BLAST-Like Alignment Tool (blat) output (psl format).

iGUIDE_manuscript_analysis

Analysis provided in the "iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity" manuscript.

nuckit

[Dev] Nucleotide sequence analysis took kit - command line utilities for managing large volumes of nucleotide sequences based in the R-programming language.

acquireIntSites

[Internal] Retrieve intSites from db given a single GTSP number or a string in a .csv file or patient ID in a .csv file.

chiva

[Dev] Combined HIV integration site and genomic variant analysis pipeline.

spraphal

[Dev] R-package for assistance with sparse graphical analysis.

tsap

[Dev] Software pipeline for targeted sequencing of genomic DNA samples.

add_uniqRegion_to_sampleInfo

[Internal] Adds the uniqRegion column to sampleInfo.tsv files used by intSiteCaller

cloneTracker

[Depreciated, see gintools repo] Utility functions for analysis of integration site datasets.

consolidate_longitudinal_data

[Internal] Consolidate longitudinal data between patients within the specified database.

contamCheck

[Internal] Check intSiteCaller output for crossover between different samples which may be contamination.

dualDemultiplexR

[Depreciated, see nuckit repo] Demultiplex Illumina FASTQ files using dual barcodes (I1 and I2).

EpigeneticHeatmapMaker

filterRootSeqReads

[Internal] Filter reads that appear in a subset of output sequence files from the original sequencing file based on read names

flank

[Code Review] Examples for using GenomicRanges::flank().

genomicHeatmapMaker

getAbundStats

[Internal] Get abundance summary stats from a group of integration site data.

github_tutorial

A hands on forking, cloning, pulling, pushing, merging tutorial.

homebrew-cask

A CLI workflow for the administration of Mac applications distributed as binaries

intSiteCheckR

[Internal] Generate summary table of most abundant clones present within given specimens.

makeSampleInfo

[Internal] Generate sampleInfo.tsv for intSiteCaller from databased information

makeUCSCHubFromBedFiles

make customer UCSC genome browser hub from bed files

postCallerIDFilter

[Internal] Filter output from IntSiteCaller by IDs and resort filtered reads to their correct replicate

seqConsolidateR

[Depreciated, see nuckit repo] Consolidate nucleotide sequences to unique sequences with a key.

seqFiltR

[Depreciated, see nuckit repo] R-based tool for filtering a sequence file based on supplied indices or another sequence file.

seqTrimR

[Depreciated, see nuckit repo] Trims 5' and 3' nucleotide sequences from paired-end reads.

simIntSiteReads