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Garrett Graham's Projects

aect icon aect

A deep learning based pipeline for TSS coverage denoising and feature extraction from shallow cell free DNA sequencing

autoconf-archive icon autoconf-archive

A mirror of the GNU Autoconf Archive, a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet.

bax2bam icon bax2bam

Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format

bprna icon bprna

bpRNA: Large-scale Annotation and Analysis of RNA Secondary Structure

bwa-meth icon bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

cuttlefish icon cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.

deeptools icon deeptools

Tools to process and analyze deep sequencing data.

desso icon desso

A DL-based framework for sequence and shape motif identification in the human genome

ggh4x icon ggh4x

ggplot extension: options for tailored facets, multiple colourscales and miscellaneous

ggsashimi icon ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

griffin icon griffin

A flexible framework for nucleosome profiling of cell-free DNA

hisat2 icon hisat2

Graph-based alignment (Hierarchical Graph FM index) (SIMDe)

kmc icon kmc

Fast and frugal disk based k-mer counter

last icon last

Copy of the last aligner

macs icon macs

MACS -- Model-based Analysis of ChIP-Seq

memes icon memes

An R interface to the MEME Suite

methyldackel icon methyldackel

A (mostly) universal methylation extractor for BS-seq experiments.

miso icon miso

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

mixcr icon mixcr

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

outrigger icon outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

paragraph icon paragraph

Graph realignment tools for structural variants

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