GitHub topics: bioinformatics-analysis

Repositories

LionNite/Youtube-Tutorial

Build a crypto arbitrage bot for passive income. Explore the code, test it out, and watch the tutorial on YouTube! 🚀💻

Size: 61.5 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

m13paiva/HULK

HULK is a fully automated, containerized pipeline for processing bulk RNA-seq data directly from SRA accessions

Language: Python - Size: 4.71 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

algbio/flowpaths

A Python package to quickly decompose weighted graphs into weights paths, under various models.

Language: Python - Size: 2.27 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 7 - Forks: 4

gbif/hp-asean

Biodiversity Informatics and Geospatial Analysis, ASEAN Centre for Biodiversity

Language: HTML - Size: 208 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 2

twoXes/awesome-structural-bioinformatics

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Language: Python - Size: 31.1 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 74 - Forks: 10

RipollJ/awesome-bioinfo-tools

A curated list of awesome Bioinformatics tools.

Size: 13.7 KB - Last synced at: 6 days ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1

ValldHebron-Bioinformatics/minMutFinder

Tool written in Python and Bash implemented in a Nextflow pipeline that accurately identifies mutations and assesses their frequencies, accounting for multiple nucleotide mutations occurring within a single codon. Additionally, it can annotate mutations associated to phenotypical changes in viral populations based on user-supplied datasets.

Language: Python - Size: 79.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

DEBOPRIYA2320/FASTA-File-Analysis-using-Shell-Scripting

This repository contains a collection of shell scripts designed for analyzing DNA sequences stored in FASTA files. Each script demonstrates the use of Unix/Linux command-line tools and shell programming concepts such as loops, conditionals, and pattern matching.

Size: 3.15 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

NorwegianVeterinaryInstitute/DemultiplexRawSequenceData

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards

Language: Python - Size: 501 MB - Last synced at: 16 days ago - Pushed at: 17 days ago - Stars: 2 - Forks: 0

sebastianstupak/biolens-old-idea

Bioinformatics CLI tool for analysis and visualization

Language: Rust - Size: 764 KB - Last synced at: 17 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

Elliot-Chan-120/GEM

GEM | Gene Edit Machine: A machine learning-enhanced platform capable of classifying and optimizing gene variants for reduced pathogenicity. Featuring multi-database integration, research-backed feature engineering, optimized DNA and Protein-level analyses, and an intelligent guided + stochastic mutation algorithm "ReGen".

Language: Python - Size: 40.7 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 1 - Forks: 0

lynnlangit/gcp-for-bioinformatics

GCP for Bioinformatics Researchers

Language: Jupyter Notebook - Size: 89.9 MB - Last synced at: 29 days ago - Pushed at: 5 months ago - Stars: 277 - Forks: 74

HMShahzaib/bioseq_analyzer

An interactive Python toolkit for DNA, RNA, and protein sequence analysis — including alignments, nucleotide counting, transcription, complements, and reverse sequences.

Language: Python - Size: 6.23 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

HMShahzaib/protein-physicochemical-properties

A Python tool to compute physicochemical properties of proteins from FASTA files. Supports molecular weight, isoelectric point (pI), instability index, aliphatic index, and GRAVY score using Biopython.

Language: Python - Size: 8.79 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

conorheffron/global-max-sim-matrix

Compute Global Maximum Similarity Matrix for 2 Sequences

Language: R - Size: 257 KB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

jneyareddy/MSc-Thesis-Data

High-quality genome annotations for Torulaspora delbrueckii LO544, Lachancea thermotolerans IWBT Y1240, and Chlorella sorokiniana (wine-related origin). Structural and functional annotation files are provided, enabling exploration of strain-specific genomic features and supporting downstream omics and biotechnological applications.

Size: 4.88 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

marcellobeltrami/AMResistance

A predict AMR based on protein or DNA sequences

Language: Jupyter Notebook - Size: 3.25 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

BU-ISCIII/buisciii-tools

set of helper tools for bu-isciii management of its core services portfolio.

Language: Python - Size: 39.3 MB - Last synced at: 18 days ago - Pushed at: 19 days ago - Stars: 2 - Forks: 17

BioContainers/containers

Bioinformatics containers

Language: Dockerfile - Size: 8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 746 - Forks: 256

GuyTeichman/RNAlysis

Analyze your RNA sequencing data without writing a single line of code

Language: Python - Size: 797 MB - Last synced at: 9 days ago - Pushed at: 5 months ago - Stars: 139 - Forks: 13

andrewgull/tga_detection

Code for detection of tandem gene amplifications in ultra-deep long read sequencing data

Language: Python - Size: 26.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

microbioinformatic/Functional-Enrichment-Studio

BioInfo Tools

Size: 3.91 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

BioJulia/GenomeGraphs.jl

A modern genomics framework for julia

Language: Julia - Size: 16.4 MB - Last synced at: 15 days ago - Pushed at: over 5 years ago - Stars: 69 - Forks: 7

DuttonLab/kvasir

Searching for Horizontal Gene Transfer

Language: Python - Size: 32.7 MB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 10 - Forks: 5

adenger/subpred3

Code for the manuscript "Optimized data set and feature construction for substrate prediction of membrane transporters"

Language: Jupyter Notebook - Size: 50.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

Bilmem2/TaxoConserv

A web-based platform for statistical analysis and visualization of evolutionary conservation scores across taxonomic groups.

Language: Python - Size: 9.18 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

greenelab/multi-plier

An unsupervised transfer learning approach for rare disease transcriptomics

Language: HTML - Size: 119 MB - Last synced at: 25 days ago - Pushed at: almost 6 years ago - Stars: 45 - Forks: 11

alaimos/mithril-standalone

This repository hosts the java implementation of MITHrIL and SPECIFIC

Language: Java - Size: 258 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

SouradiptoC/CodonU

A python project for analysis of codon usage for gene or genome analysis

Language: Python - Size: 64.4 MB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 23 - Forks: 1

LabOnoM/DK.BeesGO

Digitized-Knowledge for BSGOU

Language: TypeScript - Size: 9.49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

cemileblks/dss-analysis

DNA Methylation patterns detection analysis as a part of my MSc Bioinformatics Dissertation Project.

Language: Shell - Size: 1.62 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

cinnetcrash/gelidonyamr

This Nextflow pipeline, gelidonyAMR, has been developed for analyzing Salmonella Infantis genomes, including genome assembly, antimicrobial resistance (AMR) profiling, MLST and cgMLST typing. It is designed for use in a Conda environment and is part of the my PhD project

Language: Nextflow - Size: 3.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

NikitaArya17/next_generation_sequencing_projects

A collection of independent research projects involving various methods involving next generation sequencing (NGS) data analysis, including scRNA-seq, RNA-seq and scATAC-seq data.

Language: Jupyter Notebook - Size: 32.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

SimonHegele/rnaQAUSTcompare

Small python CLT that generates a comparative plot for multiple rnaQUAST reports

Language: Python - Size: 4.31 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

mhtjsh/covid19-scRNAseq-Tcell-analysis

Analysis pipeline for single-cell RNA sequencing (scRNA-seq) data focused on T cells in COVID-19. Includes scripts and workflows for data processing, visualization, and identifying immune cell signatures and responses. Designed to accelerate reproducible research in immunology and single-cell genomics.

Language: Jupyter Notebook - Size: 178 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Language: Python - Size: 3.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 24 - Forks: 4

FabbriniMarco/microbAIDeR

An ensemble of functions for easier and quicker preliminary microbiome analyses

Language: R - Size: 282 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

a-fsh-r/AML_Microarray_Analysis_An_Introduction_to_Bioinformatics_Project

My solutions for the project of "An Intro to Bioinformatics" - Sharif University of Technology (SUT) - Prof. Somayyeh Koohi and Prof. Ali Sharifi-Zarchi - Fall 2021(1400-1).

Language: R - Size: 6.83 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Eduardodelpinotoro/NonCodingRNA-CHEK2-Splicing-AI

Size: 622 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

BioContainers/specs

BioContainers specifications

Size: 479 KB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 52 - Forks: 12

Georgakopoulos-Soares-lab/taxonomic_quasi_primes

Repo for the biological analyses performed on taxonomic quasi-prime peptides.

Language: Python - Size: 3.49 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

xqwen/fastenloc

Colocalization analysis of genetic association signals

Language: C++ - Size: 154 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 52 - Forks: 12

jhtullis/Blast_Classification

Train random forest, k-nearest neighbors to classify blasts from RLs

Language: Jupyter Notebook - Size: 29.8 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

JhuangLab/BioInstaller

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

Language: R - Size: 2.92 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 57 - Forks: 12

sheffield-bioinformatics-core/spatial_transcriptomics_tutorial

A bare bones tutorial on how to analyse spatial transcriptomics data from raw sequencing reads to visualising spatially distinct features

Language: HTML - Size: 150 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 0

cohenoa/biosignalen

"BioSignaLen," a computational tool designed for the rapid identification of response variations across different conditions in large datasets, hence enhancing the understanding of computational analysis outcomes and suitable for various computational studies.

Language: Python - Size: 12.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

rajanbit/Archive

Archive of all the tools and pipelines

Language: Python - Size: 174 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1

urmi-21/pyrpipe

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

Language: Python - Size: 204 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 84 - Forks: 28

adenger/subpred_dl

Code for the manuscript "Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction".

Language: Jupyter Notebook - Size: 21.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

Size: 178 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 17 - Forks: 1

jefferyUstc/WTF-Bioinformatics

collection of bioinformatics tools and tips, maybe | 生物信息学软件工具、分析tips集合

Size: 19.5 MB - Last synced at: 19 days ago - Pushed at: over 4 years ago - Stars: 16 - Forks: 1

pritampanda15/YouTube-Tutorials

Tutorials on bioinformatics, computational biology, molecular dynamics, and other specialized scientific tools and workflows.

Size: 2.95 MB - Last synced at: 11 days ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0

Sushmithaa1234/amr-trend-analysis

Visualization and Forecasting of AMR trends using WHO GLASS dataset

Language: Jupyter Notebook - Size: 507 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Aridoge13/Computational_Biology

Independent Computational Biology Projects

Language: Python - Size: 1.31 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

V-Z/hybseq-course

Materials for course about processing HybSeq data on computing grids

Language: TeX - Size: 1.63 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

thom22/Predicting-Colorectal-Cancer-IO-Therapy-Outcomes-via-ML-using-MSI-and-Gene-Mutation-Status

This work was completed as part of a research project at Johns Hopkins University.

Size: 146 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

IdoBar/Mespilia_transcriptome_analysis

Transcriptome analysis pipeline of sea urchin larvae

Language: HTML - Size: 0 Bytes - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

IdoBar/Papaya_fruit_transcriptome_analysis

Transcriptome analysis pipeline of ripe papaya fruit to determine flavour-determining genes

Language: HTML - Size: 1.86 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

V-Z/hybseq-scripts

Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

Language: Shell - Size: 2.35 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 2

mansikath/Variant-calling

Repository for variant calling utilizing bioinformatics tools and databases

Size: 10.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

BU-ISCIII/iskylims

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Language: Python - Size: 22.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 75 - Forks: 39

dvklopfenstein/ReactomePy

Explore biomolecular pathways in Reactome from the command-line or a Python script

Language: Python - Size: 17.1 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 4

UmbertoDellaMonica/fp-mash

Fp-Mash contains an adaptation of the Mash tool specifically designed to process fingerprints as part of the lyn2vec project. The main objective is to leverage the capabilities of Mash for fast and efficient genome and metagenome distance estimation, and apply these features to the vectorization tasks in lyn2vec

Language: C++ - Size: 42.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

SWAROOP006/NGS-Variant-Calling

This project focuses on identifying somatic variants in whole-genome sequencing (WGS) data from tongue cancer samples and cell lines. The workflow leverages industry-standard tools for alignment, quality control, and variant calling, specifically targeting chromosomes 6 and 7 of the human genome.

Language: HTML - Size: 1.94 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

SWAROOP006/Machine-Learning-in-Bioinformatics-using-WEKA

Used WEKA machine learning tool to analyze the Breast cancer data and also study Protein characteristics using SMO, naïve byes and IBk models also, data bias was removed using bagging and stacking. R program was used to extract the character-specific protein sequences using the R package PROTr and peptide.

Language: R - Size: 129 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

mikeph52/GC-Genie

GC-Genie is a GC percentage calculator written in C++.

Size: 20.5 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

renatosantos98/ont-benchmark

Supporting data for the publication "Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing"

Language: Jupyter Notebook - Size: 199 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

vipese/GeneticAssociation

Pipeline for genetic association analysis designed for Stanford University Mignot Lab

Language: Roff - Size: 416 KB - Last synced at: 4 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

fomightez/humap3-binder

Using data from hu.MAP 3.0 with the convenience of Python and Jupyter.

Language: Jupyter Notebook - Size: 1.03 MB - Last synced at: 4 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

bobeobibo/phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

Language: HTML - Size: 6.8 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 52 - Forks: 15

ulelab/peka

Find motifs enriched around prominent crosslinks

Language: Python - Size: 31.9 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2

SevdanurGENC/Bioinformatics-with-Biopython-Lecture-Notes

This repo contains Bioinformatics lecture notes using Biopython.

Language: Jupyter Notebook - Size: 34.6 MB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 20 - Forks: 0

fomightez/pdbepisa-binder

Using data from PDBePISA with the convenience of Python and Jupyter.

Language: Jupyter Notebook - Size: 1.48 MB - Last synced at: 2 months ago - Pushed at: 12 months ago - Stars: 7 - Forks: 1

ElsaB-Lab/Fandrei_et_al_2025

Supplementary code for the analysis of Fandrei et al. Clinical Cancer Research 2025

Language: Jupyter Notebook - Size: 5.63 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

pierrepo/PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

Language: Python - Size: 50.9 MB - Last synced at: 23 days ago - Pushed at: almost 5 years ago - Stars: 29 - Forks: 15

bioinfocz/scdrake

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.

Language: R - Size: 11.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 11 - Forks: 2

ZealousGeneticist/cartoflow

A Python workflow for taking chemicals, finding the genes they interact with, and mapping the communities of genetic interactions.

Language: Python - Size: 63.5 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

cox-labs/CoxLab_Bug_Reporting

MaxQuant and Perseus Bug Reporting

Size: 24.4 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 7 - Forks: 1

royalseeker/hackbio-biocoding-internship

HackBio Internship

Language: Jupyter Notebook - Size: 1.21 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

oicr-gsi/sarsCoV2Analysis

Classify samples as being either SARS-CoV-2 positive or negative, identify the strain of virus, and produce statistics about the mapping.

Language: WDL - Size: 188 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

AramPapaz/MetaTIS

Predicting eukaryotic translation initiation

Language: Python - Size: 21.6 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

FabrizioG202/biodart 📦

An effort to develop a Bioinformatics Toolkit in pure-dart.

Language: Dart - Size: 70.3 KB - Last synced at: 8 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

uc-bd2k/GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

Language: HTML - Size: 38.2 MB - Last synced at: 6 months ago - Pushed at: over 6 years ago - Stars: 49 - Forks: 19

filipsPL/degronopedia-ml-psi

Predict Protein Stability Index from the sequence

Language: Python - Size: 7.21 MB - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 5 - Forks: 0

ScialdoneLab/CIARA_python

Implementation of entropy of mixing algorithm in python

Language: Jupyter Notebook - Size: 327 KB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 1

imrobintomar/protein-sequence-analysis

A Python-based tool for analyzing protein sequences and calculating various physicochemical properties. This tool uses BioPython's ProtParam module to analyze FASTA sequences and exports the results to an Excel file.

Language: Python - Size: 10.7 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

cvigilv/ResidueFisher

Bioinformatics protocol that aims at mining information at the sequence and structure level of protein chain to detect possible evolutionary conserved residues.

Language: Python - Size: 33.3 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1