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249 search results found

☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Protein Transformer ⭐ 25

Predicting protein structure through sequence modeling

10 Simple Rules Data Storage ⭐ 24

A repository for the 10 simple rules data sharing paper to be submitted to PLoS Comp Biology

Regulatory Prediction ⭐ 24

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

Teaching ⭐ 24

Code and files used in teaching and training courses.

Soap3 Dp ⭐ 24

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

Fastheatmap ⭐ 23

Super high performance interactive heatmap software

🌎 Review materials for bioinformatics, computational biology, and science in general

A Python Framework for Modeling and Analysis of Signaling Systems

The Microbiome Interpretable Temporal Rule Engine

Symmetry ⭐ 22

🎡 Detect, analyze, and visualize protein symmetry

Data visualization library for creating interactive graphs and dashboards for bioinformatics etc.

Smart search engine for all bioinformatics databases worldwide

Patchsim ⭐ 21

Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.

KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.

Aptasuite ⭐ 20

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

Teaching ⭐ 20

Courses & workshops led by members of the Krishnan Lab.

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Heatmapgenerator ⭐ 19

Cross-platform GUI desktop application for making biological heatmaps

Slamdunk ⭐ 18

Streamlining SLAM-seq analysis with ultra-high sensitivity

Screenlamp ⭐ 18

screenlamp is a Python toolkit for hypothesis-driven virtual screening

Team Rosalind Project ⭐ 18

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Microscope ⭐ 17

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

Biosemble ⭐ 17

AI assembly of bioNLP wordnets

Bioinformatics ⭐ 17

Course materials for Computational Biology and Bioinformatics - BI462

Doctoral Thesis ⭐ 17

Generation and Applications of Knowledge Graphs in Systems and Networks Biology

A Python toolkit for setting up benchmarking dataset using biomedical networks

Computational Cryoet ⭐ 16

A curated list of awesome computational cryo-ET methods.

SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Asapdiscovery ⭐ 15

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

Diff Evol Tree Search ⭐ 15

We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.

Bio Phylo ⭐ 15

Bio::Phylo - Phyloinformatic analysis using Perl

MuRaL is a deep learning framework for estimating single-nucleotide mutation rates across the genome.

Escherconverter ⭐ 14

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Hypothesis Bio ⭐ 14

Hypothesis extension for computational biology

Brendapyrser ⭐ 14

A Python parser for the BRENDA database

Sars Cov 2_b.1.1.529_spike Rbd_predictions ⭐ 14

AlphaFold2 and RoseTTAFold predictions of the SARS-CoV-2 B.1.1.529 variant Spike protein with HADDOCK antibody interactions

Patient-Specific Modeling in Python

DeepSEA in TensorFlow

GEMINI: A variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens

Bioinformatics Conf Vids ⭐ 13

List of conferences with talk videos posted online

pyABC: distributed, likelihood-free inference

Biosimulators ⭐ 13

Registry of containerized biosimulation tools that support a standard command-line interface

Query sequence database by HMMs arranged in predefined synteny structure

Toolchest Client Python ⭐ 13

Toolchest Python client

Alife Data Standards ⭐ 13

Repository to host data standards for the ALIFE community.

Phylotoast ⭐ 12

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

Compbio Gists ⭐ 12

Computational Biology & Bioinformatics Resources

A Tutorial for Parallelised Scalable Simulations in TensorFlow

Keypoint Diffusion ⭐ 12

A diffusion model for structure-based drug design with faster inference from learned representations of protein structure.

Intro2compbio ⭐ 12

An undergraduate class on introduction to computational biology by Professor Shao Li.

Ammolite ⭐ 12

Visualize structure data from Biotite with PyMOL

Ultrafast sequence typing and gene detection from NGS raw reads

Isambard ⭐ 11

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

Robust Paper ⭐ 11

Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

Repository for my research on generative modelling of cell images

Epidemic ⭐ 11

EPIDEMIC is an easy-to-run educational toolkit for epidemiological analysis.

Zincbinddb ⭐ 10

The database and API backend for ZincBind - the database of zinc binding sites

A bare metal Python library for building and manipulating protein molecular structures

Guidescan Cli ⭐ 10

A gRNA database generation tool.

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Pgp_reconstruction ⭐ 10

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

iCodon customizes gene expression based on the codon composition

An implementation of the Locally Scaled Diffusion Map (LDFMap) dimensionality reduction technique.

Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

Autopacmen ⭐ 10

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Alphabeta ⭐ 10

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Discovering de novo shared transcriptional programs in single cancer cells

Randomwalkrestartmh ⭐ 10

A package to perform Random Walk with Restart on different types of networks

Py4lifesci ⭐ 9

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

Intro_to_wc_modeling ⭐ 9

Whole-cell modeling tutorials

A Docker-based packaging system for platform-agnostic implemented algorithms

PCA on Genotypes

Open Science ⭐ 9

curated links and customized materials to support biomedical researchers in implementing open science approaches

Compbio_on_git ⭐ 9

My computational biology course as it evolves in real time

This python code creates hybrid MD/MC (NAMD/GOMC) simulations for the NVT, NPT, GCMC, and GEMC-NVT ensembles

Artisanal 🤣 bioinformatics tools and pipelines in Scala

Computational biology packages for Go.

Programming and numeric computing platform for math modeling and visualization with fully functional programming language

Team Greider ⭐ 8

Main repository for the HackBio'2021 Virtual Internship Experience for #Team-Greider ❤️

This is a curated list of tutorials, projects, libraries, videos, papers, books and anything related to applications of Deep Learning to biomedicine. Feel free to make a pull request to contribute to this list.

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

Embeddings to Network Alignment - align biological networks between two species

Genextender ⭐ 8

R/Bioconductor package for optimized functional annotation of ChIP-seq data

Multi-Atom Structure/Selection Toolkit with Interaction Capabilities

Julia Theosysbio ⭐ 8

Cryo Ralib ⭐ 8

Lgatto.github.io ⭐ 8

Scripts to prepare and analyze molecular dynamics simulations

MD DaVis: A python package to analyze molecular dynamics trajectories of proteins

Siteinterlock ⭐ 8

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

101-200 of 249 search results

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