GitHub topics: bioinformatics-scripts

Repositories

LabOnoM/DK.BeesGO

Digitized-Knowledge for BSGOU

Language: TypeScript - Size: 9.54 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours 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: 173 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 17 - Forks: 1

joseiky/Data-analytics

Python codes used for analyzing large datasets for machine learning, statistics, data cleaning and structuring, visualizations, etc.

Language: Python - Size: 14.7 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

pritampanda15/YouTube-Tutorials

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

Size: 2.95 MB - Last synced at: 5 days ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

Aridoge13/Computational_Biology

Independent Computational Biology Projects

Language: Python - Size: 1.31 MB - Last synced at: 15 days ago - Pushed at: 15 days 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: 22 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

tomarovsky/Biocrutch

Various bioinformatics scripts

Language: Python - Size: 1.6 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 8 - Forks: 1

Ashley-Milton/MEU-SHA-histone-mods

Language: R - Size: 21.5 KB - Last synced at: 26 days ago - Pushed at: 27 days 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: 28 days ago - Pushed at: 28 days ago - Stars: 4 - Forks: 2

RPINerd/biox_macguffins

A loose collection of random scripts I've generated over the years

Language: Python - Size: 195 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

Ashley-Milton/OAN-epigenetic-profiling

Language: R - Size: 44.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

biotorrents/biophp Fork of kennypavan/BioPHP

BioPHP implements some light tools for manipulating genomic data

Language: PHP - Size: 124 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

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: 3 days ago - Pushed at: 3 days 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: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

vidboda/MDUtils

Utilities for MobiDetails

Language: Python - Size: 948 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

mikeph52/GC-Genie

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

Size: 20.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

vinuesa/TIB-filoinfo

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

Language: Shell - Size: 160 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 22 - Forks: 5

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: 2 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

widdowquinn/find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.

Language: Python - Size: 95.8 MB - Last synced at: 28 days ago - Pushed at: over 1 year ago - Stars: 61 - Forks: 24

fomightez/sequencework

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

Language: Python - Size: 3.74 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 24 - Forks: 4

Alepidoptera7/MissingMotif

Determines the most probable sequences missing from a greater set of genomic reads.

Language: Python - Size: 7.81 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

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: 3 months ago - Pushed at: 3 months ago - Stars: 2 - 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: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

dvklopfenstein/ReactomePy

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

Language: Python - Size: 17.1 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 23 - Forks: 4

fomightez/pdbepisa-binder

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

Language: Jupyter Notebook - Size: 1.48 MB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 1

pwwang/biopipen

A set of processes/pipelines for bioinformatics

Language: R - Size: 42.7 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 13 - Forks: 5

royalseeker/hackbio-biocoding-internship

HackBio Internship

Language: Jupyter Notebook - Size: 1.21 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

QmLHS/SAMBA

Saving Apples with MetaBarcoding Analysis

Language: Python - Size: 178 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

SouthGreenPlatform/GeMo

A mosaic genome painting tool for plant genomes

Language: JavaScript - Size: 8.89 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 15 - Forks: 1

Abibsb/Master_thesis

Recopilación de los resultados y herramientas generadas para la tesis de maestría "Estudio de la relación estructura-función en interfaces de complejos RNA-proteína", SBG-UNQ

Language: Python - Size: 5.71 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Aaryesh-AD/Sequence-cluster-consensus

Scripts for clustering protein sequences, generating consensus sequences that represent a common representative of the cluster, and identifying representative medoid sequences for each cluster as the sequence most representing the cluster.

Language: Jupyter Notebook - Size: 5.48 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

lucahennet/RNAseqWorkflow

Detection of differentially expressed genes from bulk RNA-seq data

Language: Shell - Size: 12.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

IBCHgenomic/bacterial-KO-phylogenomics

analyzing bacterial genome based ontologies and phylogenomics informativeness

Language: Python - Size: 2.46 MB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

IBCHgenomic/BIGG-metabolic-analyzer-API

a API to BIGG metabolic databases

Language: Python - Size: 189 KB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

HuffordLab/NAM-genomes

Detailed bioinformatics scripts and methods used in the NAM genome paper.

Language: R - Size: 138 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 74 - Forks: 29

mhtjsh/ROSALIND-Problems

I am curating a my own solution repository take to Rosalind Questions. I feel Rosalind question are the Leetcode website which curates the best question to generally solve and attack the understanding part of the algorithms with the mix of Biology.

Language: Python - Size: 22.5 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

tony-zhelonkin/RNAseq_pipelineDock Fork of bschiffthaler/ngs

RNAseq preprocessing docker

Language: Shell - Size: 2.66 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1

V-Z/structure-sum

Script to summarize the results from several structure runs

Language: R - Size: 28.3 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

jnbdz/bio-quickstarts

🦠 Biology (bioinformatic, biology, bio-hacking, etc) | Quickstarts 🦠

Size: 2.39 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

fomightez/pdbsum-binder

Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org

Language: Jupyter Notebook - Size: 140 KB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

adeschen/mpileupTools

This python script parses a mpileup file to extract the coverage of each base at each position.

Language: Python - Size: 34.2 KB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 2

SUGAM2001/DESeq2-Python-Example

This repository contains an example implementation of DESeq2 in Python.

Language: Python - Size: 2.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

bioinfonupeb/lbcm-patricia-snps

SNPs selection for QTL study.

Language: Python - Size: 1.03 MB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

conorheffron/global-max-sim-matrix

Compute Global Maximum Similarity Matrix for 2 Sequences

Language: R - Size: 250 KB - Last synced at: 4 days ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

alfonsomiguelcruz/pgc_btip_topone

TopONE is a project that studies recombination events using topological data analysis. This was made in the PGC-BTIP 2024 internship by Alfonso Miguel Cruz and Claire Angelie Gabisay, and mentored by C.J. Palpal-latoc.

Language: Python - Size: 32.7 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 3 - Forks: 0

minesh1291/HowToBioinformatics

:man_scientist: Analysis Pipelines and Useful Tools

Language: R - Size: 8.45 MB - Last synced at: 6 days ago - Pushed at: almost 7 years ago - Stars: 8 - Forks: 1

bystrogenomics/bystro

Bystro genetic analysis (annotation, filtering, statistics)

Language: Python - Size: 73 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 40 - Forks: 13

flystar233/pyscript-bio

生物信息学python代码，专注于重测序文本计算、处理

Language: Python - Size: 122 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 24 - Forks: 6

jfrojasc/Bioinformatics

R reports about bioinformatics tasks

Language: HTML - Size: 720 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

cbp44/samflags

Command line utility written in NodeJS to decode SAM flags to explain what they mean.

Language: JavaScript - Size: 7.81 KB - Last synced at: 1 day ago - Pushed at: almost 8 years ago - Stars: 4 - Forks: 0

Dogth/biomultitool

GUI for a few tools

Language: JavaScript - Size: 66.8 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

hansen-han/ena_rnaseq_quantification

Tool for easily downloading and quantifying RNAseq data from the European Nucleotide Archive (ENA) with Salmon.

Language: Python - Size: 30.3 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

Funny-Silkie/bayes-mapper

Maps the evaluation value of phylogenetic tree to another tree

Language: Python - Size: 22.5 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

ulelab/peka

Find motifs enriched around prominent crosslinks

Language: Python - Size: 31.9 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 2

roseedwin/Benchmarking-taxonomic-classifiers-for-soil-shotgun-data

Benchmarking various taxonomic classifiers for profiling soil metagenomic data, with scripts and tools tailored for fungal, bacterial, and archaeal genome identification.

Language: R - Size: 4.23 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

chrisarg/alien-seqalignment-edlib

Sequence Alignment tool

Language: Perl - Size: 43 KB - Last synced at: 1 day ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

arendsee/bioinfo-utils

A gallimaufry of questionable shellscripts

Language: Shell - Size: 103 KB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 1

tgolubch/castanet

Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.

Language: Python - Size: 27.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 1

danangcrysnanto/bovine-graphs-mapping

Comparison of sequencing read mapping to pangenome graphs

Language: Jupyter Notebook - Size: 8.21 MB - Last synced at: 22 days ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 2

asadprodhan/Bioinformatics_Educational_Resources

Bioinformatics Educational Resources

Size: 149 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

jakobilab/bioinfo-scripts

Assorted scripts in Perl, Bash, R and whatsoever directly from a bioinformatician's scripts/ folder

Language: Shell - Size: 170 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

mdcjansen/CNNs

Various codes and scripts used during AI research. Orginally developed in the Binary_label_predictions_with_CNNs repository

Language: Python - Size: 47.9 KB - Last synced at: 29 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

thuylinhmk/Histone-Modification-Networks

histone modification hospot

Language: Python - Size: 8.56 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

parisepigenetics/rna_feat_ext

Software tools to extract mRNA's features from a list of ENSEMBL gene IDs.

Language: Python - Size: 127 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

cinnetcrash/Biyoinformatik_TR

Bu sayfada Biyoinformatik analizler ile ilgili eğitim materyalleri bulunmaktadır.

Language: Shell - Size: 18.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

Seb943/Smith_Waterman_Py

Implementing the Smith-Waterman algorithm in Python

Language: Python - Size: 13.7 KB - Last synced at: 17 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

Matthew-Mosior/Fasta-Region-Inspector-OLD 📦

A Haskell script that performs knuth-morris-pratt string search across a region of fasta file for ambiguity codes, and determines whether variants are found in ambiguity codes.

Language: Haskell - Size: 40.8 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

wintergenomics/wbs-rbioinfo

R es un lenguaje básico de referencia en el mundo de la estadística y una herramienta fundamental para el análisis de datos en el área de las ciencias de la vida. R permite automatizar los cálculos estadísticos y la generación de diversos gráficos para facilitar el análisis de datos.

Language: CSS - Size: 1.23 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

alitermos/FastQC_processor

This script streamlines the processing of '.qc files' in bulk by utilizing the 'fastqc command', and organizing the output into a specifically designated folder named 'qc_reports_pretrim'. This facilitates the management and analysis of quality control for sequence data.

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

foriin/Piccolo

A little script that looks for piRNA clusters based on small RNA library coverage

Language: C++ - Size: 2.46 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

foriin/SuRoQ

A pipeline for quick and dirty QC of your small RNA-seq libraries focused on piRNA.

Language: C++ - Size: 12.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

hasimhko/AlignStatExtract

Python scripts that extract alignment statistics from the output text files of HISAT2 and Samtools, and organize them into CSV files.

Language: Jupyter Notebook - Size: 314 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-parasail

Sequence Alignment tool

Language: Perl - Size: 31.3 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-last

Sequence Alignment tool

Language: Perl - Size: 37.1 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-hmmer3

Sequence Alignment tool

Language: Perl - Size: 24.4 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-mmseqs2

Sequence Alignment tool

Language: Perl - Size: 29.3 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-bowtie2

Sequence Alignment tool

Language: Perl - Size: 32.2 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-minimap2

Sequence Alignment tool

Language: Perl - Size: 20.5 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

alvesrco/pipecov

This project proposes to contribute to fill the knowledge gap about Covid-19SARS-CoV-2 in Brazil and with the global knowledge about the pathogen. The scientific community and governments of other countries are looking for actions along these lines. The United Kingdom recently established a research network for genomic studies of SARS-CoV-2Covid-19 with a contribution of GBP 20 million (https://www.gov.uk/government/news/uk-launches-whole- genome-sequence-alliance-to-map-spread-of-coronavirus).

Language: R - Size: 28.3 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 12 - Forks: 8

boyinthebigcity/AmideSearch

A comprehensive analysis of putative neuropeptide precursors in the proteome database.

Language: Jupyter Notebook - Size: 413 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mrdanieleze/Genomic-Sequence-Comparison-Code-GSCC-

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

Language: Python - Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

johnnytam100/pdb2uniprot

A Python script to map PDB ID + chain ID to UniProt ID.

Language: Python - Size: 15.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

xlq902/FAFSA-combine

This is a program written in c# for neat organization of FASTA files into one file to make multiple sequencing alignments easier.

Language: C# - Size: 9.77 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

akanksharawat07/Bio_Rscripts

Rscripts_for_datahandling

Language: R - Size: 2.97 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

AlkaffAhamed/Modified-K-Means-on-PDB-File

An implementation of modified K-Means clustering on Biological Data (Proteins).

Language: R - Size: 70.3 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

hzz0024/BioinfoTools

Introduction to CBSU server. A library of bioinformatics tools for data analyses and visualization.

Language: R - Size: 3.08 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

norael-zein/bioinf

This is a collection of scripts for the bioinformatic analysis in the bachelor's thesis "Exploring the Potential of Camelid Single-Domain Antibodies: Structure, Properties and Diverse Applications in Therapeutics and Diagnostics" (2023). The scripts have been developed by Nora El-Zein, Nora Hemmingsson and Sara Mosebach.

Language: Python - Size: 413 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0