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box2dpolymer

Simulations of polymers in two dimensions based on the Box2D physics engine

catadata

dna_ode

Simulating DNA using coarse-grained Langevin molecular dynamics

genome-ai

Artificial Intelligence to detect from which genome a sequence comes from

hpip

Hundreds of promoters in parallel project

interactivesims

Jupyter notebooks for showing and analyzing interactive simulations

kldna

C library to compute electrostatic potentials of Kornyshev-Leikin theory of DNA-DNA interactions

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mybiotools

Python tools for working with biological data

mylib

Fast and portable C libraries for performing calculations using GSL and various usual tasks.

mymakefiles

Makefile templates

mystat

Command-line tool to perform basic statistics

myvimconf

my NeoVIM configuration

myvmdtools

my scripts and configuration files for VMD

nucpos

A research project on the effect of sequence on the positioning of nucleosomes in vivo

pr_peaks

Project on quantitative analysis of Progesterone Receptor ChIP-seq peaks

pubmed-lookup

Lookup PubMed records and make Publication objects with info about a scientific publication

pybruno

Python utilities to use Bruno markup language files

sbs_tracers

Code to generate an analyze simulations for the paper "Theoretical principles of transcription factor traffic on folded chromatin"

sc_hiv

sesame-manuscript

Manuscript for the Sesame library

shrec3d

shortest-path reconstruction in 3D

snippets

Snippets of code and various instructions that come handy here and there

starcode

All pairs search and sequence clustering

tf-kinetics

Code and text of my project on transcription factor kinetics.

tissue-ai

Artificial intelligence to understand RNA expression patterns in different tissues

triplib

Code to analzye TRIP data

wlc

C library to compute worm-like chain polymer functions

zerone

ChIP-seq discretization and quality control