samuelmiver Goto Github PK

circos

Running some examples and tests learning to use the Circos genome visualization tool.

compbiozurich.github.io

A resource of the Zurich bioinformatics and computational biology community

crispr_app

CRISPR detection web application

crispr_detection

Scripts and results from the project of sequence analysis of the Mycoplasma pneumoniae genome looking for potential 20-mers to target CRISPR interruption processes. Project developed for the Centre for Genomic Regulation, under the guidance of Alicia Broto, Maria Lluch and Luis Serrano.

derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data

diffraction

Diffraction includes several functions to work and perform differential analysis over pile ups coming from non fractionated RNASeq analysis.

dn-ds

Calculates the ratio of non-synonymous mutations per non-synonymous site, to synonymous mutations per synonymous site, given a sequence of DNA. This can be used as a metric for characterising selection on a region of DNA.

dynamicalmodelingmethods

Mount Sinai - Dynamical Modeling Methods for Systems Biology (March 2014)

elmseq

excelerate-ttt

Materials for ELIXIR-EXCELERATE Train The Trainer workshops and courses

exhaustive

Python library to support exhaustive testing and model checking

initiation_kinetics

Model for kinetic model of transcription initiation

insysbio

MATLAB scripts to simulate examples of biological systems exposed in the book "An Introduction to Systems Biology", written by Uri Alon.

java818avaj

Several scripts and courses to learn Java programming

jupyter

Repository containing Jupyter Notebooks for most of the blog posts on my blog. For example, there are data visualization, data manipulation, and data analysis code examples in the Notebooks

killswitch

Defining variants (SNPs, insertions and deletions) for a set of HiSeq samples exploring the variability in populations of M. pneumoniae transformed with a killswitch cassette

kinetic_manuscript

Kinetic paper

learn_c_the_hard_way

Code and scripts written following the book "Learn C the Hard Way" (http://c.learncodethehardway.org/book/)

learning_whole_cell

repo to learn the basics in github

matlab818baltam

Several trials and scripts learning and controlling MATLAB

matrix-curses

matrix code animation for curses - see how deep the rabbit-hole goes

membrane_builder

A membrane builder script using bash, tcl and vmd

mysql818lqsym

Some trials in order to learn basics in MySQL

nussinov

nussinovs algorithm for RNA secondary structure prediction

overlapy

Project for the subjects of Structural Bioinformatics and Python (M.Sc. in Bioinformatics)

protinseq

A transposon sequencing protocol that selects insertions in-frame to expressed genes

pymodel

Model-based testing in Python

pyr4ml

Python and R scripts to perform basic Machine Learning approaches

python-machine-learning-book-2nd-edition

The "Python Machine Learning (2nd edition)" book code repository and info resource

pyutils

Some basic python functions