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amt-biped-analysis

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bedtools2

A powerful toolset for genome arithmetic.

bigdataformats

bioinflatexstyles

Bibtex compatible latex templates for a selection of Bioinformatics and Genomics journals

bioinformatic_algorithms

bioinformatic_algorithms

bioinformatics

Tools for bioinformatics

bioinformatics-algorithms-coursera

Solutions to Programming Assignments for Bioinformatics Algorithms (Part 1) on Coursera.org

bioinformatics-training

Bioinformatics training resources

dplyr

Plyr specialised for data frames: faster & with remote datastores

ffrancis.github.io

format-conversion

Convert the formats of files used in Bioinformatic analysis

hotnet2

HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

image_feature_detection

Detect and mark face and eye features in images using openCV, python

jbrowse

A modern genome browser built with JavaScript and HTML5.

julia-mit

Tutorials and information on the Julia language for MIT numerical-computation courses.

l.d._vs_genomicdistance

An R package to calculate and plot mean linkage disequilibrium (L.D.) over genomic distance

linkagedisequilibrium_decay

Linkage disequilibrium vs physical distance multi-plotting in R with local regression smoothing

machine_learning_regression

ml-class

Machine learning programming exercises

model_gdnasizedistand3prime_pmol_calc

Model the fragment size distribution of B73 (Maize) gDNA based on fragment analyzer result and calculate the picomole amount of DNA for that particular distribution of DNA fragment size.

multiple-sequence-alignment-shannon-s-entropy

Parse multiple sequence alignment out put files and calculate Shannon's entropy for each column of the alignment

network_snps

A framework for network analysis and display of SNPs

ngs-phagedisplay

Machine Learning pipeline for NGS's phage display data

non_exome_mask

Parse Exon and Mask non-exonic regions in the repeat and polymorphism masked sequences or any other sequences

other_analysis_codes

Other_analysis_codes_biomix

pacbioeda

Python scripts for Exploratory Data Analysis of Pacific Biosciences sequence data

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

parsemaizehapmap2data

Python script to extract insertions, deletions and SNPs(IUPAC format) from Maize B73 HapMap2 data, for specified coordinates and chr_no

pbdagcon

A sequence consensus algorithm implementation based on using directed acyclic graphs to encode multiple sequence alignment