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aerial

Aerial graph/model db

aerial.bio.utils

Various bioinformatic general utility tools for unified file reading, sequence xform, sequence entropy information processing , et.al.

aerial.fs

General file system utility functions (eg, dodir cpfiles, generalized move, etc). Extended from an original work of Miki Tebeka

aerial.utils

Various utility functionality covering common tasks; trees; clustering; graphs; probability, stats, and information theory, et.al.

aerobio

Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.

aerosaite

Saite delivered as self installing / running uberjar

aeroviews

Instrumented interactive visulizations for Aerobio sequencer data analyses

bam.iobio.io

http://bam.iobio.io

bbhanami

Bare Bones example Hanami client/server app

clj-iobio

A robust, flexible, full program DAG, declarative tool definition, extensible toolset iobio server in Clojure. With function nodes, streaming and non streaming flow, dynamic caching, logging, and superior error handling.

cljs-adventures

Various experiments using all manner of ClojureScript stuff (re-com, reagent, reframe, quil, etc)

dmm

Data Flow Matrix Machines. Generalization of recurrent neural networks.

gaisr

Genomic Analysis Illuminating Structured RNA

hanami

Interactive arts and charts plotting with Clojure(Script) and Vega-lite / Vega. Flower viewing 花見 (hanami)

hanasu

A very light weight, simple websocket based messaging system in Clojure(Script). Converse/talk 話す(hanasu).

js-binary-vcf-tabix

JavaScript BGZF VCF and binary Tabix readers

js-bv-common

Javascript common functionality across tabix and bai index file processing

js-bv-sampling

Javascript read depth and random sampling on bai (bam) and tba (vcf/tabix) index file and binary readers

js-local-bam

Javascript local BAM and BAI index file parsing and processing

js-local-vcf

Javascript local VCF and Tabix index file parsing and processing

jsa-aerial.github.io

jsbgzf

Javascript bgzf inflation and deflation

md-to-hiccup

Convert markdown to hiccup in one pass

msgpacket

Client<->Server/Peer<->Peer message protocol and implementations

packages

Javascript libraries packaged up with Google Closure externs

panclus

Pangenome clustering using entropy, relative entropy, cumulative RE, hybrid distributions, et.al

pyhanasu

Hanasu for Python

saite

Interactive document creation for exploratory graphics and visualizations. 咲いて (in bloom). Built on top of hanami vega/vega-lite library with CodeMirror and self hosted ClojureScript

scribl

bioinformatic canvas-based chart library

seqsim

An approach to various sequence (genes, amplicons, ncRNA, et. al) similarity via informed embeddings, matrices, and LA