Sean Gordon's repositories
rpackages
R package development - the Leek group way!
bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
PyVCF
A Variant Call Format reader for Python.
CNS
expand on joshua's CNS project
goatools
Python scripts to find enrichment of GO terms
genomicspapers
The Leek group guide to genomics papers
LittleInferenceBook
A book for the coursera statistical inference class
data-day-examples
Example notebooks for running the Spark and Machine Learning Examples
Joshua-Levy-Synteny-Analysis
Integrated Analysis of Synteny (Multiple Synteny Comparison for Multiple Alignment, Circos Outputs, Allmaps Genome Reconstructions), Find Ghost Genes, Identify and Analyze CNS Elements from Multiple Alignment Files and More!
capitalIn21stCenturyinR
Piketty in R
regmodsbook
A companion book for the Coursera Regression Models class
transcriptome_microsats
Scripts used in evaluating microsatellite loci developed from transcriptomes
estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
dataanalysis
The lecture slides for Coursera's Data Analysis class
jcvi_062915
add on features, keep current with master
courses
Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1
datasharing
The Leek group guide to data sharing
jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
Caffo-Coursera
A repository of my Coursera latex code and notes
angio-pulse
Analysis code for Angiosperm diversification rate paper
jcvi-bin
Collection of third-party softwares used in jcvi library
treecut
Find nodes in hierarchical clustering that are statistically significant
read_mapping_to_pangenome_matrix
A Python Script to Automate Mapping Short Reads to Draft Genomes - Then, by the grace of Computer God, Calculate the Number of Reads Per Homologue Accorded to Get_Homologues Output
get_homologues_to_pathway-tools
Python scripts to convert the .faa output from the software package "get_homologues" back to .gbk file necessary for analyses using Pathway-tools
MathematicsBiostatisticsBootCamp2
The github repository for mathematical biostatistics bootcamp 2
Rmarkdown_JSviz
Short tutorial on knitr/markdown and JS visualization libraries googleVis and rCharts