Mike Lin

sqlite_zstd_vfs. SQLite3 extension for read/write storage compression with Zstandard

GenomicSQLite. Genomics Extension for SQLite

PhyloCSF. Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

sqlite_web_vfs. SQLite3 extension for read-only HTTP(S) database access

spVCF. Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently

gfabase. GFA insert into GenomicSQLite

iitii. Implicit Interval Tree with Interpolation Index

should.ml. Literate assertions for OCaml

forkwork. OCaml library for forking child processes to perform work on multiple cores

twt. The Whitespace Thing for OCaml

gvcf_norm. gVCF allele normalizer

node-assert-type. Concise runtime type assertions for Node.js

ocaml-sqlite3EZ. Thin wrapper for sqlite3-ocaml with a simplified interface

GLnext. Scalable gVCF merging and joint variant calling

vcf_line_splitter. Split a huge VCF file into parts, quickly

blogging-my-genome. DNAnexus platform applets for analyzing my genome, and associated notes

CRF. OCaml library for semi-Markov conditional random fields

miniwdl-cloud. SUPERSEDED BY https://github.com/miniwdl-ext/miniwdl-aws

ocaml-bgzf. OCaml library for BGZF, a gunzip-compatible format allowing random access to the uncompressed data

miniwdl. A static analysis toolkit for the Workflow Description Language

c9-ocaml. Installation script for OCaml and OPAM inside a Cloud9 IDE workspace

stakesign. Sign files via blockchain + put your money where your mouth is

yaxpo. Yet Another XML Parser for OCaml

mlin-ocaml-genomics. Mike Lin's OCaml Genomics library

yajl-ocaml. OCaml bindings for the YAJL streaming JSON parser

RocksWorm. Access RocksDB databases over HTTPS for write-once/read-many use cases

RGenomicSQLite. [WIP / not yet ready] R bindings package for GenomicSQLite

pfda2dockstore. Export precisionFDA apps to Dockstore

ounit. Unit tests for OCaml (mirror of darcs repository)

opam-repository. Package descriptions for OPAM

transcriptformer. Jupyter Notebook

GenomicSQLite-examples. C

dxMAF. DNAnexus platform apps for working with MAF cross-species genome alignments

20140411-dxjc-wgs-variant-calling. Presentation for DNAnexus journal club on Heng Li's WGS variant calling preprint

fastp. An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

CDE. CDE: Code, Data, and Environment packaging for Linux