mym88mym's repositories
ThinkStats2
Text and supporting code for Think Stats, 2nd Edition
RTCGA
Download, integration and visualizations of the variety & volume of TCGA data.
NSF-BioSketch-template
LaTex template for NSF biographical sketch
filter_contigs
Simple BioPython toy to filter contigs based on size. Used highly-Pythonic "generator" design - ideal for adaptation to stream processing.
gdc-client
GDC Data Transfer Tool
book
Compiled and pretty version of labs
pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
361Division
361 Division - Scientific Training, Education and Learning
dedup
Deduplication for cfDNA sequencing data
ezmap
NGS pipeline for viral metagenomics analysis
basic_UNIX_2015
basic UNIX workshop materials and files
htseq
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
myTCGA
It's just a personal record for studying how to analysis TCGA data(expression+mutation+methylation+CNV)
cfncluster
CfnCluster is a framework that deploys and maintains HPC clusters on AWS.
lesson_format
Lesson formatter
Pic2Text
A script to transform picture to text
comp-genomics-class
Code and examples for JHU Computational Genomics class
copycat
Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
fasta_utilities
A collection of scripts developed to interact with fasta, fastq and sam/bam files.
ChIP-seq-analysis
ChIP-seq analysis notes from Tommy Tang
dailyprogrammer
Solutions to chosen Reddit Daily Programmer challenges.
jhu_int_prog
Publicly visible materials for intermediate programming
coursera_genpython_final
Final exam project developed during "Python for Genomic Data Science".
coursera_ads
Homework (Python) and notes for the course Algorithms for DNA Sequencing that is offered by John Hopkins School of Medicine (October 2015)
MIT6.00.1x-Introduction-to-Computer-Science-and-Programming-Using-Python
my notes for the homework
ads1-notebooks
Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing