bioinformatics
Repositories (1438)
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
A collection of publications on comparison of high-throughput sequencing technologies.
DeepSEA in TensorFlow
Software packages for smart growing environments.
DriverPower
An R package for reproducible and automated ADMIXTOOLS analyses
The BridgeDb Library source code
Toolkit for preparing genomes for submission to NCBI
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
Some useful python scripts for biologists
A Python package for drug discovery by analyzing causal paths on multiscale networks
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
Collection of YouTube videos on data science on the Data Professor YouTube channel.
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
Materials for the Training and Engagement Website
A tool for projecting genomic alignments to transcriptomic coordinates
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that cons...
Zavolan-Lab Automated RNA-Seq Pipeline
Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets. KG4SL is the first graph neural network (GNN)-based m...
Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
Stacked Denoising AutoEncoder based on TensorFlow
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
Data and analysis for the Splatter paper
programs and scripts, mainly python, for analyses related to nucleic or protein sequences
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Fork of the Polysolver project
SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.
3D printed sculpture of a DNA molecule, showing my own genome
exploratory and interactive microbiome analyses based on heatmaps
This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️
Compute N50/NG50 and auN/auNG
A comprehensive pipeline for short read metagenomic data
Generate interactive dotplot from mummer4 output using plotly
Method to optimally select samples for validation and resequencing
A collection of modules and sub-workflows for Nextflow
Important bioinformatics algorithms as well as other useful scripts
GRAph-based Finding of Individual Motif Occurrences
R package – HLA Genotype Imputation with Attribute Bagging (development version only)
A case study on Pfam dataset to classify protein families.
CiteFuse:
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS da...
Visual Machine Learning of Genome-Phenome Associations
GEDFN: Graph-Embedded Deep Feedforward Network
Command line tools for CMDB varaints browser
DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm