samuelmiver

fastqins

Pipeline for transposon sequencing processing

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.

EXCELERATE-TtT

Materials for ELIXIR-EXCELERATE Train The Trainer workshops and courses

membrane_builder

A membrane builder script using bash, tcl and vmd

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

pyutils

Some basic python functions

RanSEPs

RanSEPs provides a framework for genome re-annotation and novel small proteins detection adjusting the search to different genomic features that govern protein-coding capabilities

raspi_games

Classic games developed under the python package pygame and running in a Raspberry Pi

rosalind.info

Here are some scripts written in python to solve biological problems proposed in rosalind.info

samuelmiver/RanSEPs

RanSEPs provides a framework for genome re-annotation and novel small proteins detection adjusting the search to different genomic features that govern protein-coding capabilities

samuelmiver/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.

samuelmiver/EXCELERATE-TtT

Materials for ELIXIR-EXCELERATE Train The Trainer workshops and courses

samuelmiver/rosalind.info

Here are some scripts written in python to solve biological problems proposed in rosalind.info

samuelmiver/SysMIC

Scripts developed following the text book of SysMIC course in Systems Biology (http://sysmic.ac.uk/moodle/)

samuelmiver/TempLaTex

Templates for latex

samuelmiver/circos

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

samuelmiver/protinseq

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

samuelmiver/pyutils

Some basic python functions

samuelmiver/compbiozurich.github.io

A resource of the Zurich bioinformatics and computational biology community

samuelmiver/diffraction

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

samuelmiver/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.

samuelmiver/ELMSeq

samuelmiver/exhaustive

Python library to support exhaustive testing and model checking

samuelmiver/initiation_kinetics

Model for kinetic model of transcription initiation

samuelmiver/JAVA818AVAJ

Several scripts and courses to learn Java programming

samuelmiver/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

samuelmiver/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

samuelmiver/kinetic_manuscript

Kinetic paper

samuelmiver/learn_C_the_hard_way

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

samuelmiver/learning_whole_cell

repo to learn the basics in github

samuelmiver/MATLAB818BALTAM

Several trials and scripts learning and controlling MATLAB

samuelmiver/MYSQL818LQSYM

Some trials in order to learn basics in MySQL

samuelmiver/PyR4ML

Python and R scripts to perform basic Machine Learning approaches

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

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

samuelmiver/pyvenn

2 ~ 6 sets venn diagram for python

samuelmiver/RNIE

A package for predicting Rho independent terminators in bacterial genomes

samuelmiver/RUFFUS818SUFFUR

samuelmiver/samuelmiver.github.io

samuelmiver/tech_test