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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.

add_uniqregion_to_sampleinfo

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

blatcoupler

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

cart19_intsite_manuscript_analysis

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

chiva

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

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.

gintools

[Dev] Tools for genomic DNA integration analysis

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

iguide

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

iguide_manuscript_analysis

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

intsitecaller

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

nuckit

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

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

spraphal

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