xtmgah/data-science-at-the-command-line
Data Science at the Command Line
Developer Profile
xtmgah
Discovered public repositories for xtmgah in the GitHub catalog.
xtmgah/phypapers
info and 'how to' on setting up twitterbots to post academic papers
xtmgah/dplyr-tutorial
Public repository.
xtmgah/broom
Convert statistical analysis objects from R into tidy format
xtmgah/samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
xtmgah/vawk
An awk-like VCF parser
xtmgah/shinyTree
Shiny integration with the jsTree library
xtmgah/statebins
Alternative to choropleths of US States ala http://bit.ly/statebins
xtmgah/tidyr
Easily tidy data with spread and gather functions.
xtmgah/bioruby-vcf
Smart VCF parser
xtmgah/ggthemr
Themes for ggplot2.
xtmgah/dendextend
R package
xtmgah/verticalize
Simple tool to verticalize text delimited files.
xtmgah/MitoSeek
Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing
xtmgah/bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
xtmgah/bam-readcount
count DNA sequence reads in BAM files
xtmgah/org.caleydo.vis.lineup.demos
LineUp Demos
xtmgah/broman
R/broman: A package with Karl Broman's personal R code
xtmgah/d3_bis
pdf graph to interactive graph with d3 and inkscape
xtmgah/nozzle
Nozzle is a report generation toolkit for data analysis pipelines implemented in R.
xtmgah/qqman
R code for creating Manhattan plots and Q-Q plots for GWAS
xtmgah/BeQTL
Bootstrap eqtl
xtmgah/THetA
Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.
xtmgah/Paradigm
PAthway Representation and Analysis by Direct Inference on Graphical Models
xtmgah/ffs
Schemas to convert common fixed-width file formats into CSV using in2csv.
xtmgah/csvkit
A suite of utilities for converting to and working with CSV, the king of tabular file formats.
xtmgah/bioawk
BWK awk modified for biological data
xtmgah/sga
de novo sequence assembler using string graphs
xtmgah/gridvar
GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format.
xtmgah/labs
Scripts for the PH525x: Data Analysis for Genomics
xtmgah/BESST
BESST - scaffolder for genomic assemblies
xtmgah/estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
xtmgah/bedtools-protocols
Public repository.
xtmgah/samtools-utilities
Utilities for Samtools ( http://samtools.sourceforge.net/ )
xtmgah/ccsandbox
some C++ programs
xtmgah/viewFusion
View fusion event by circos plot
xtmgah/RNASeqDEPipeline
RNA-Seq differential gene expression pipeline
xtmgah/pileup2base
Parse samtools pileup file to get how many bases and what kind of bases are called
xtmgah/filo
Useful FILe and stream Operations
xtmgah/reviews
Writing reviews of academic papers
xtmgah/assemblathon2-analysis
collection of scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 entries (assemblies)
xtmgah/rvtests
Rare variant test software for next generation sequencing data
xtmgah/vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
xtmgah/solarplot
Mitochondrial Solar Plot
xtmgah/oneliners
Useful bash one-liners for bioinformatics.
xtmgah/rCharts_nvd3_perf
Public repository.
xtmgah/INF-BIO9120_fall2013_de_novo_assembly
Course material for the de novo assembly part of the INF-BIO9120 course at Univ. of Oslo Fall 2013
xtmgah/d3examples
Examples of interactive graphics using d3.js
xtmgah/Rmarkdown_JSviz
Short tutorial on knitr/markdown and JS visualization libraries googleVis and rCharts
xtmgah/jheatmap
Javascript Heatmap viewer