593 Open source projects that are alternatives of or similar to PCG

The Ensembl Compara Perl API and SQL schema

Official git repository for Biopython (originally converted from CVS)

Phylogenetic trees in Julia

A fast whole-genome aligner based on de Bruijn graphs

Version 5 of the CAFE phylogenetics software

Genotyping of segregating mobile elements insertions

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Read DNA sequences from colourful Microsoft Word documents

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Mapping-Assisted Targeted-Assembly for Metagenomics

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Scripts used for my UseR!2015 presentation on the network structure of CRAN

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Fast alignment and preprocessing of chromatin profiles

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Genomics data visualization in Python by using matplotlib.

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Assembling the cause of phenotypes and genotypes from NGS data

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Stacked Denoising AutoEncoder based on TensorFlow

An optimized graphs package for the Julia programming language

VirNet: A deep attention model for viral reads identification

A library to build and execute typed scientific workflows

My own tools code for NGS data analysis (Next Generation Sequencing)

React rerelease of MSAViewer

🚦 Run Picard on BAM files and collate 90 metrics into one file.

A curated list of awesome bioinformatics software.

Predict plasmids from uncorrected long read data

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Processor scripts for Wikipedia dumps to crush them into a dense binary format that is easy to pathfind with.

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

📊 Identify cell types and pathways affected by genetic risk loci.

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Introduction to the Unix Shell for biologists

Per-base per-nucleotide depth analysis

Examples using Clustergrammer2 to explore high-dimensional datasets.

Data Structures and Algorithms

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

A computational library for learning and evaluating biological knowledge graph embeddings

No description or website provided.

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Provide R access to the NCI Genomic Data Commons portal.

Interactive Graph Visualization in Your Browser

Useful bioinformatic scripts

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

GWAS summary statistics files QC tool

This repo conatins the code of the problems practised by me on Codeforces,Codedchef,Leetcode,Geeks For Geeks

Rapid determination of appropriate reference genomes.

Implementation of various Data Structures and algorithms - Linked List, Stacks, Queues, Binary Search Tree, AVL tree,Red Black Trees, Trie, Graph Algorithms, Sorting Algorithms, Greedy Algorithms, Dynamic Programming, Segment Trees etc.

An open-access bioinformatics text

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

exploratory and interactive microbiome analyses based on heatmaps

Unsupervised domain adaptation method for relation extraction

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

Fast motif matching in R