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datasciencer

a curated list of R tutorials for Data Science, NLP and Machine Learning

deep-learning-with-python-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deepcontact

DeepContact Software

deepcov

Fully convolutional neural networks for protein residue-residue contact prediction

deepnovo

Protein Identification with Deep Learning

deepsequence

A generative latent variable model for biological sequence families.

deeptime

Deep learning meets molecular dynamics.

diamond

Accelerated BLAST compatible local sequence aligner.

embeddings_reproduction

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

evcouplings

Evolutionary couplings from protein and RNA sequence alignments

fastcluster

Fast hierarchical clustering routines for R and Python.

frameshift

freesasa

C-library for calculating Solvent Accessible Surface Areas

ggplot2

An implementation of the Grammar of Graphics in R

github

GitHub 漫游指南- a Chinese ebook on how to build a good build on Github. Explore the users' behavior. Find some thing interest.

gmx_tutorials_livecoms

LiveCoMS GROMACS Tutorials Paper

gromacs

Public/backup repository of the gromacs molecular simulation toolkit

gromacswrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, all with the same Python code) into python scripts.

hbec_sars-cov-2_scrna-seq

Supplementary data for "Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells"

hh-suite

Remote protein homology detection suite.

hivtrace

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers

hyphy

HyPhy: Hypothesis testing using Phylogenies

icelogo

Next-generation visualization of protein consensus sequences by iceLogo.

ifeature

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.

igphyml

A phylogenetic analysis program designed for B cell receptor sequence data. It implements the HLP17 codon substitution model which is capable of accounting for unusual features of affinity maturation such as context dependent hotspot mutations, nonreversible sequence evolution, and descent from a known germline sequence. Based off of codonPhyML.

interproscan

intro_to_r