rfinkers

html5-boilerplate

A professional front-end template for building fast, robust, and adaptable web apps or sites.

rstudio

RStudio is an integrated development environment (IDE) for R

rdflib

RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

jvarkit

Java utilities for Bioinformatics

gatk

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

assemblage

Tools for working with second gen assemblies, fasta sequences, etc

bamUtil

fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:

juicebox_scripts

A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats

pauvre

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

DataFAQs

LINKED DATA QUALITY REPORTS

hagfish

Hagfish - assess an assembly through creative use of coverage plots

crammer

Reference-based compression of SRA data

VariantToolChest

VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful tools: (1) SetOperator for performing powerful set operations; and (2) VarStats for various statistics on VCF files.

nanopub-java

Java library for nanopublications based on RDF4J

Crop-Ontology

An ontology database for crops' traits with their variables

RepARK

Repetitive motif detection by Assembly of Repetitive K-mers. RepARK is free for academic and non-profit use. By downloading you agree with the FLI-LICENSE included in the package.

KentLib

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This may contain some of my own libraries for bioinformatics utilities as well as long as they install easily on both my mac and linux box.

PhenotypeDatabase

Phenotype Database

Breakpointer

Breakpointer is a fast algorithm to locate breakpoints of structural variants from single-end reads produced by next-generation sequencing.

galaxy-pcr-markers

Scripts for design of PCR-based Marker Assays from DNA sequence variant data, plus Galaxy xml files

MIAPPE-ontology

Modelling of MIAPPE

jChebi2gene

Java library to automatically link a chebi compound/identifier to a metabolic pathway or genes from the tomato genome.

rfinkers.github.com

Personal github page

tomatogenome

Project directory for the analysis of ancient tomato DNA

omicsFusion

OmicsFusion is a web application which can perform univariate regression and a number of modern regression techniques and then ranks the predictors according to an importance criterion (mean rank over all the methods) so that in the visualization the top list contains the most important predictors.