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2015-07-09-iceland

Template for workshop websites.

diffpath

findinginfo

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

khmer-protocols

ngs_analysis

Scripts for analysis of MiSeq/HiSeq data: quality control, mapping, and so forth.

pathwayanalysis

Finding differentially expressed pathways from RNAseq data

scar_manuscript_scripts

Scripts for analyses of scar data and data visualization, identifying evolutionarily independent isolates, and enumerating population level unique scar occurrences

scartrek

Python package for identifying genetic changes in whole-genome sequencing data

scikit-learn

scikit-learn: machine learning in Python

shell-novice

Software Carpentry introduction to the shell for novices.

simulation

Simulate Illumina next-gen reads to determine the settings that will allow detection of rare variants (freq 0.001).

snptb

A Bioinformatics Pipeline for Analyses of Mycobacterium tuberculosis Whole Genome Sequencing Data

tb_latency_scripts

Scripts for data analysis, SNP incidence modeling, dN/dS calculation

theproj

Test project for software carpentry

variantreconstruct

Constructing genomic variants from Illumina reads of a mixed population