569 Open source projects that are alternatives of or similar to Hicexplorer

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

A library for generating an interactive SVG visualization of CWL workflows

Version 5 of the CAFE phylogenetics software

Versatile open-source tool for microbiome analysis

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

🎯 Human transcription factor target genes.

Workflow Description Language - Specification and Implementations

Ploidy agnostic phasing pipeline and algorithm

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

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UNCURL is a tool for single cell RNA-seq data analysis.

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C++ library and cmdline tools for parsing and manipulating VCF files

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Single-Cell Analysis in Python. Scales to >1M cells.

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

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No description or website provided.

A full spaCy pipeline and models for scientific/biomedical documents.

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

Signal-level algorithms for MinION data

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Guided synteny alignment between duplicated genomes (within specified quota constraint)

PERF is an Exhaustive Repeat Finder

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Curated list of bioinformatics formats and publications

Robust and efficient workflows using a simple language agnostic approach

Estimate metagenomic coverage and sequence diversity

Build and maintain multiple custom conda environments all in once place.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Cutadapt removes adapter sequences from sequencing reads

GRAph-based Finding of Individual Motif Occurrences

Lightweight Iterative Gene set Enrichment in R

Working with molecular structures in pandas DataFrames

The BridgeDb Library source code

Benchmarking programming languages/implementations for common tasks in Bioinformatics

GNparser normalises scientific names and extracts their semantic elements.

🐣 locally query the ncbi taxonomy

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Tools and databases for analyzing HLA and VDJ genes.

Bioinformatics one liners from Ming Tang

The START App: R Shiny Transcriptome Analysis Resource Tool

Javascript full-stack framework for Big Data visualisation and analysis

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

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

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

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FastQC port to Qt5: A quality control tool for high throughput sequence data.

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Project metadata manager for PEPs in Python