Most popular bioinformatics repositories and open source projects

cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing b...

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PhyloFisher

PhyloFisher is a software package written in Python3 that can be used...

12   25   25  

zarp

Zavolan-Lab Automated RNA-Seq Pipeline

5   25   25  

KG4SL

Synthetic lethality (SL) is a promising gold mine for the discovery of...

8   25   25  

nf-LO

A Nextflow workflow to generate lift over files for any pair of genome...

7   25   25  

mixs

Minimum Information about any (X) Sequence” (MIxS) specification

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qtip

Qtip: a tandem simulation approach for accurately predicting read alig...

7   24   24  

genomedisco

Software for comparing contact maps from HiC, CaptureC and other 3D ge...

9   24   24  

StackedDAE

Stacked Denoising AutoEncoder based on TensorFlow

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SeqMaker.jl

(No maintenance) Next Generation Sequencing Simulation with SNP, Varia...

10   24   24  

splatter-paper

Data and analysis for the Splatter paper

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sequencework

programs and scripts, mainly python, for analyses related to nucleic o...

5   24   24  

scanPAV

Pipeline to detect PAVs (presence/absence variations) in genome compar...

7   24   24  

hla-polysolver

Fork of the Polysolver project

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SNPbinner

SNPbinner is a utility for the generation of genotype crossover points...

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dna-sculpture

3D printed sculpture of a DNA molecule, showing my own genome

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calour

exploratory and interactive microbiome analyses based on heatmaps

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team-rosalind-project

This is the main repository for the HackBio'2020 Virtual Internship Ex...

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calN50

Compute N50/NG50 and auN/auNG

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MetaSUB_CAP

A comprehensive pipeline for short read metagenomic data

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CellBench

R package for benchmarking single cell analysis methods

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mummer-idotplot

Generate interactive dotplot from mummer4 output using plotly

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SVCollector

Method to optimally select samples for validation and resequencing

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BioNextflow

A collection of modules and sub-workflows for Nextflow

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Bioinformatics-Algorithms

Important bioinformatics algorithms as well as other useful scripts

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GRAFIMO

GRAph-based Finding of Individual Motif Occurrences

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HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (developmen...

6   23   23  

Protein_Sequence_Classification

A case study on Pfam dataset to classify protein families.

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TestingPackage

A Simple R Package Illustrating Components of an R package: 2019-2022...

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helpful_commands

Command-line tools, commands, and code snippets for performing routine...

12   23   23  

CiteFuse

CiteFuse:

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haploclique

Viral quasispecies assembly via maximal clique finding. A method to re...

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GenAMap

Visual Machine Learning of Genome-Phenome Associations

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GEDFN

GEDFN: Graph-Embedded Deep Feedforward Network

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cmdbtools

Command line tools for CMDB varaints browser

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DeepChem-Workshop

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biolog...

12   22   22  

lightdock-python2.7

Protein-protein, protein-peptide and protein-DNA docking framework bas...

9   22   22  

mview

MView extracts and reformats the results of a sequence database search...

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varsome-api-client-python

Example client programs for Saphetor's VarSome annotation API

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mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

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kmer-counter

Count kmers with a more efficient (faster) hash table

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RNA-Science-Toolbox

A platform to do RNA science

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berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

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ena-cog-uk-wfs

Collection of scripts for automated SARS-CoV-2 genome surveillance.

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pm4ngs

Project Manager for NGS data analysis

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sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

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countminsketch

An implementation of Count-Min Sketch in Golang

4   22   22  

review

:earth_americas: Review materials for bioinformatics, computational bi...

1   22   22  

croissance

Tool for estimating growth rates from microbial growth curves

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MetagenomeScope

Visualization tool for (meta)genome assembly graphs

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