samuelmiver
Postdoctoral bioinformatics researcher @SushiLab // Past: PhD in computational biology in Design of Biological Systems (Serrano Lab) at @CRG-CNAG
ETH-Zurich
Pinned Repositories
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's Repositories
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