shulp2211

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Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

2 10

AnnotationPipeline-EVM_based-DClab

Cantù Lab @ UC Davis - Annotation pipeline - EVM based

Language:Python1 10

cov2tree

Cov2Tree website, based on Taxodium

Language:HTML100

covtobed

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

Language:C++MIT1 10

google-research

Google Research

Language:Jupyter NotebookApache-2.0100

HaploSync

Tools for haplotype-wise reconstruction of pseudomolecules

Language:Python1 10

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

Language:TeX1 10

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Language:PythonGPL-3.01 10

kent

UCSC Genome Browser source tree. Stable branch: "beta".

Language:CNOASSERTION100

ldsc

LD Score Regression (LDSC)

Language:PythonGPL-3.0100

ML-YouTube-Courses

A repository to index and organize the latest machine learning courses found on YouTube.

1 10

models-1

Model zoo for genomics

Language:PythonMIT100

Monopogen

Single Cell Population Genetics and Association Analysis Tool

Language:Python100

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language:NimMIT100

neuromaps

A toolbox for comparing brain maps

Language:PythonNOASSERTION100

paraphase

HiFi-based SMN1 and SMN2 caller

Language:PythonBSD-3-Clause-Clear100

pb-16S-nf

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

Language:NextflowBSD-3-Clause-Clear100

pb-human-wgs-workflow-snakemake

Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads

BSD-3-Clause-Clear100

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Language:JavaMIT1 10

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Language:PythonMIT100

PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)

Language:Jupyter NotebookMIT100

rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

GPL-3.0100

scEvoNet

scEvoNet is a tool for generation a cell type - gene program network between species or different time points in the same organism.

Language:Jupyter NotebookMIT100

scRNA-seq_notes

A list of scRNA-seq analysis tools

Language:RMIT100

simCAS

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data

Language:Jupyter NotebookGPL-3.0100

single_cell_pipeline

Single Cell Analysis Automated Workflow

Language:PythonGPL-3.0100

STAR-Fusion

STAR-Fusion codebase

Language:PerlBSD-3-Clause1 10

taxonium

Explore very large trees in the browser

Language:JavaScript100

usher

Ultrafast Sample Placement on Existing Trees

Language:C++MIT100

yahs

Yet another Hi-C scaffolding tool

MIT100