441 Open source projects that are alternatives of or similar to conda-env-builder

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Real-time species-typing visualisation for nanopore data.

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

Assembling the cause of phenotypes and genotypes from NGS data

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Predict plasmids from uncorrected long read data

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Bystro genetic analysis (annotation, filtering, statistics)

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Ploidy agnostic phasing pipeline and algorithm

Fast alignment and preprocessing of chromatin profiles

Read DNA sequences from colourful Microsoft Word documents

Introduction to the Unix Shell for biologists

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

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

Mapping-Assisted Targeted-Assembly for Metagenomics

A computational library for learning and evaluating biological knowledge graph embeddings

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.

Useful bioinformatic scripts

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

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

A library to build and execute typed scientific workflows

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

An open-access bioinformatics text

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

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…

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.

Fast motif matching in R

Unsupervised domain adaptation method for relation extraction

Per-base per-nucleotide depth analysis

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

Genomics data visualization in Python by using matplotlib.

A fast 23andMe genome text file parser, now superseded by arv

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Guidelines for using IvLabs PC. General instructions for maintaining and using any PC/laptop while using Ubuntu for Robotics/DL/RL research.

Examples using Clustergrammer2 to explore high-dimensional datasets.

Stacked Denoising AutoEncoder based on TensorFlow

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

GWAS summary statistics files QC tool

Earl Grey: A fully automated TE curation and annotation pipeline

Rapid determination of appropriate reference genomes.

exploratory and interactive microbiome analyses based on heatmaps

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

VirNet: A deep attention model for viral reads identification

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

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

Fast and flexible ORF finder

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

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

React rerelease of MSAViewer

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

A Python platform for Structural Bioinformatics

A curated list of awesome bioinformatics software.

Method to optimally select samples for validation and resequencing

Mulled - Automatized Containerized Software Repository

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

Sentieon DNAseq

Docker images for fastai