ItzRealMePrime/AutoBLAST-Smart-MSA-Tool

🧬 Automate sequence alignment with AutoBLAST, detecting DNA, RNA, or Protein types and retrieving top NCBI matches for clear analysis.

Language: Python - Size: 1.3 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0

Nirvanazero/geneforge

🧬 Design novel proteins using AI-powered tools for drug discovery and synthetic biology with GeneForge's advanced platform.

Language: Python - Size: 1.34 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

oh-jinwoo94/gkm-align

gapped-kmer based whole genome alignment software

Language: C++ - Size: 145 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 0

Palald/mcp-sdk-typescript

🚀 Build efficient applications with the MCP SDK for TypeScript, offering optimized performance, real-time communication, and robust session management.

Language: TypeScript - Size: 246 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

inab/trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

Language: C++ - Size: 59.2 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 243 - Forks: 47

johrollin/Cont_ID

cross-contamination of plant virus base on read assignation

Language: Python - Size: 792 KB - Last synced at: about 12 hours ago - Pushed at: 6 days ago - Stars: 3 - Forks: 0

madsondeluna/AMPidentifier

AMPidentifier: A modular python toolkit for predicting antimicrobial peptides using ensemble machine learning (BR 51 2025 005859-4)

Language: Python - Size: 24.1 MB - Last synced at: 6 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 0

ShujiaHuang/mitoquest

Human Mitochondrial sequencing data Analysis Toolkit. Fetching information like variants, heteroplasmy/homoplasmy, etc. on mitochondrial genome from sequencing data

Language: C - Size: 27.8 MB - Last synced at: 5 days ago - Pushed at: 7 days ago - Stars: 5 - Forks: 0

whl-usc/rna2d3d

Scripts and reference files relevant to the computational analysis of data generated by crosslink-ligation based experiments.

Language: Python - Size: 54.4 MB - Last synced at: 5 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 1

muntisa/virsentai

Viral Sentry AI – Automated Zoonotic Surveillance & Drug Repurposing Agent

Language: Python - Size: 1.45 MB - Last synced at: 5 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

zhoutianrui-tongji/CellScope

CellScope is an unsupervised analysis framework for large-scale subcellular spatial omics data, used to systematically discover, characterize and annotate subcellular domains (subcellular domains/meta-domains) from high-resolution spatial molecular distributions.

Language: Python - Size: 2.19 MB - Last synced at: 6 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0

Bilmem2/ACMG_Assistant

A research-oriented, transparent, and extensible variant interpretation pipeline implementing ACMG/AMP 2015 & 2023 guidelines.

Language: Python - Size: 895 KB - Last synced at: 12 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 0

telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

Language: Nim - Size: 83.4 MB - Last synced at: 13 days ago - Pushed at: 14 days ago - Stars: 124 - Forks: 9

febos/SQUARNA

RNA secondary structure prediction tool

Language: Jupyter Notebook - Size: 151 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 18 - Forks: 2

Aridoge13/Computational_Biology

Independent Computational Biology Projects

Language: Python - Size: 1.32 MB - Last synced at: 14 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

hyletic/lovdtools

A fluent API client for querying the Global Variome shared LOVD instance.

Language: Python - Size: 1.64 MB - Last synced at: 15 days ago - Pushed at: 16 days ago - Stars: 1 - Forks: 0

lightdock/lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Language: Python - Size: 93.7 MB - Last synced at: 17 days ago - Pushed at: 4 months ago - Stars: 371 - Forks: 51

ncbi/tree-tool

Incremental building of phylogenetic distance trees

Language: HTML - Size: 76.1 MB - Last synced at: 17 days ago - Pushed at: 19 days ago - Stars: 27 - Forks: 10

microbioinformatic/Functional-Enrichment-Studio

BioInfo Tools

Size: 414 KB - Last synced at: 16 days ago - Pushed at: 20 days ago - Stars: 2 - Forks: 1

epifluidlab/FinaleToolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Language: Python - Size: 81.5 MB - Last synced at: 17 days ago - Pushed at: 20 days ago - Stars: 32 - Forks: 13

KarchinLab/open-cravat

A modular annotation tool for genomic variants

Language: JavaScript - Size: 9.08 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 139 - Forks: 39

m13paiva/HULK

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

Language: Python - Size: 4.83 MB - Last synced at: 7 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0

ncsa/NEAT

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

Language: Python - Size: 146 MB - Last synced at: 16 days ago - Pushed at: 19 days ago - Stars: 66 - Forks: 21

poeli/detaxa

A flexible, adaptable, and well-defined python package for taxonomy and accession number lookup.

Language: Python - Size: 331 KB - Last synced at: 18 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0

Dinesh431786/Crispr

Accelerate DNA gene editing projects with intuitive, AI-powered CRISPR gRNA design and analysis

Language: Python - Size: 315 KB - Last synced at: 18 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 0

heronoh/BLASTr

BLASTr: an R package for parallel taxonomic classification of metabarcoding sequences

Language: R - Size: 7.17 MB - Last synced at: 20 days ago - Pushed at: 23 days ago - Stars: 4 - Forks: 1

Bjorn99/Crispradium

A web application that helps researchers design optimal CRISPR guide RNA sequences. It analyzes input DNA, identifies potential target sites, and scores the guide RNAs based on factors like GC content, secondary structure, and off-target potential.

Language: Python - Size: 545 KB - Last synced at: 21 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 0

vidboda/MobiDetails

WebApp for DNA variants interpretation

Language: Python - Size: 14.2 MB - Last synced at: 24 days ago - Pushed at: 26 days ago - Stars: 14 - Forks: 6

gbif/hp-asean

Biodiversity Informatics and Geospatial Analysis, ASEAN Centre for Biodiversity

Language: HTML - Size: 208 MB - Last synced at: 26 days ago - Pushed at: 27 days ago - Stars: 1 - Forks: 2

JasonHunter95/microDNA-Detection-and-Analysis

A reproducible pipeline for detecting, extracting, and annotating small extrachromosomal circular DNA (eccDNA) from high‑throughput sequencing data.

Language: Python - Size: 2.55 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

mikeph52/BioGenie

BioGenie is a complete bioinformatics command line tool, written in C++.

Language: C++ - Size: 2.87 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 1 - Forks: 0

vihaankulkarni29/FastaAAExtractor

Language: Python - Size: 1.82 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

nyelidl/PaCS-Q

PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.

Language: Python - Size: 23.2 MB - Last synced at: 18 days ago - Pushed at: 2 months ago - Stars: 14 - Forks: 1

genotoul-bioinfo/Binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

Language: Python - Size: 937 KB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 42 - Forks: 1

rcedgar/reseek

Protein structure alignment and search algorithm

Language: C++ - Size: 68.1 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 77 - Forks: 11

liqiming-whu/pybiotk

生信常用工具合集，包括gtf/fastx/bam/bed格式文件的处理和转换，bam,bed注释工具，R绘图脚本等。

Language: Python - Size: 365 KB - Last synced at: 23 days ago - Pushed at: 29 days ago - Stars: 1 - Forks: 0

akcorut/kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Language: Python - Size: 610 KB - Last synced at: 30 days ago - Pushed at: over 1 year ago - Stars: 44 - Forks: 10

biopatternsg/biopatternsg

This project combines Generative AI and Logic AI to form an integrated process, a pipeline, that retrieves large volumes of scientific information and produces logical models that can be validated and leveraged by human experts. Our goals are to organize and to analyze knowledge with the assistance of AI and other bio-information retrieval tools.

Language: Prolog - Size: 59.8 MB - Last synced at: 21 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 1

tseemann/abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

Language: Perl - Size: 19.3 MB - Last synced at: 30 days ago - Pushed at: about 1 month ago - Stars: 459 - Forks: 100

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: 18 days ago - Pushed at: 21 days ago - Stars: 2 - Forks: 0

bcgsc/RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

Language: Java - Size: 2.41 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 107 - Forks: 9

mickaelleclercq/BioDiscML

Large-scale automatic feature selection for biomarker discovery in high-dimensional OMICs data

Language: Java - Size: 414 MB - Last synced at: 29 days ago - Pushed at: 6 months ago - Stars: 32 - Forks: 11

SouradiptoC/CodonU

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

Language: Python - Size: 64.4 MB - Last synced at: 1 day ago - Pushed at: about 1 year ago - Stars: 25 - Forks: 1

ncbi/stxtyper

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

Language: C++ - Size: 796 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 7

AtharvaTilewale/boltz2-notebook

Boltz2 Notebook – A streamlined Colab-based pipeline for protein structure prediction and binding affinity analysis using the Boltz2 deep learning model.

Language: HTML - Size: 2.22 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

ZarnackGroup/racoon_clip

racoon_clip processes your iCLIP and eCLIP data from raw files to single-nucleotide crosslinks in a single step.

Language: HTML - Size: 44.8 MB - Last synced at: 30 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 1

labstructbioinf/DeepCoil

Fast and accurate prediction of coiled coil domains in protein sequences. ​

Language: Python - Size: 154 MB - Last synced at: 30 days ago - Pushed at: about 2 years ago - Stars: 27 - Forks: 4

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: 40.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

labstructbioinf/localpdb

Python package to manage protein structures and their annotations

Language: Python - Size: 1.72 MB - Last synced at: 30 days ago - Pushed at: almost 2 years ago - Stars: 45 - Forks: 5

SimonHegele/MapSampler

Command line tool for mapping based nucleotide sequence filtering

Language: Python - Size: 500 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

yutanagano/tidytcells

Standardise TR/MH/IG data

Language: Python - Size: 40.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 3

BioAnalyticResource/ePlant_Plant_eFP

A data visualization tool to display tissue expression data for Arabidopsis thaliana

Language: JavaScript - Size: 6.37 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

satoshikawato/bio_small_scripts

Trivial utilities

Language: Python - Size: 359 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 3

amaurypm/rmsdmat

Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats.

Language: Julia - Size: 28.3 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

fethalen/better_fasta_grep

A Grep-like tool for retrieving matching sequence records from a FASTA file.

Language: Python - Size: 644 KB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 2

Vivianstats/MAAPER

Model-based analysis of APA using 3' end-linked reads

Language: R - Size: 192 KB - Last synced at: 28 days ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 5

GuoBioinfoLab/CATT

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

Language: Julia - Size: 178 MB - Last synced at: 29 days ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 4

YaoYinYing/RosettaPy

A Python utility for wrapping Rosetta command line tools.

Language: Python - Size: 929 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

rribeiro-sci/SSBtoolkit

Simulation of pharmacodynamic models of drug-GPCR (class A) interactions.

Language: Python - Size: 12.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 2

nmendozam/alleleTools

Analyze HLA and KIR alleles with this set of command-line tools

Language: Python - Size: 263 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

Gipsy-The-Sheller/YRTools

A One-for-all Plugin-based Desktop Platform for More Than Bioinformatics.

Language: Python - Size: 53.5 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

mwasifanwar/geneforge

Transformer-based system that designs novel protein structures for drug discovery and synthetic biology using evolutionary algorithms and deep learning.

Language: Python - Size: 41 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

riccabolla/PCNE

Plasmid Copy Number Estimator is a tool to estimate the copy numbers of plasmids detected in an assembled genome

Language: Shell - Size: 465 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

Superzchen/iFeatureOmega-CLI

iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versions (i.e. iFeatureOmega-Web, iFeatureOmega-GUI and iFeatureOmega-CLI) of iFeatureOmega have been made available to cater to both experienced bioinformaticians and biologists with limited programming expertise. iFeatureOmega also expands its functionality by integrating 15 feature analysis algorithms (including ten cluster algorithms, three dimensionality reduction algorithms and two feature normalization algorithms) and providing nine types of interactive plots for statistical features visualization (including histogram, kernel density plot, heatmap, boxplot, line chart, scatter plot, circular plot, protein three dimensional structure plot and ligand structure plot). iFeatureOmega is an open-source platform for academic purposes. The web server can be accessed through http://ifeature2.erc.monash.edu and the GUI and CLI versions can be download at: https://github.com/Superzchen/iFeatureOmega-GUI and https://github.com/Superzchen/iFeatureOmega-CLI, respectively.

Language: Python - Size: 8.58 MB - Last synced at: 29 days ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 11

PolyRocketMatt/diet4CoLA

Displacement and Instantaneous Edge Tracking for Cortical Laser Ablation experiments

Language: Jupyter Notebook - Size: 225 MB - Last synced at: 21 days ago - Pushed at: 23 days ago - Stars: 3 - Forks: 3

ht-diva/containers

Language: R - Size: 481 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

hermanzhaozzzz/bioat

bioat, a python package & command line toolkit for Bioinformatics and data science!

Language: Python - Size: 126 MB - Last synced at: 22 days ago - Pushed at: 2 months ago - Stars: 4 - Forks: 0

febos/urslib2

Library for processing RNA structures using PDB, DSSR and other data

Language: Python - Size: 10.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

tacclab/bio_dataset_manager

This tool facilitates the encoding of these sequences into tensors, which can then be used for AI computations and complex model implementations

Language: Python - Size: 1.86 MB - Last synced at: 4 days ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

tom-naccarato/Vis-PheWAS

A visualisation platform for analysing disease-allele associations using HLA-PheWAS data

Language: Python - Size: 33.5 MB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

DEIB-GECO/PyGMQL

Python Library for data analysis based on GMQL

Language: Python - Size: 43.4 MB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 15 - Forks: 5

lignum-vitae/biobase

A home for all biological/bioinformatics constants from protein strings to BLOSUM matrices.

Language: Python - Size: 260 KB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 11 - Forks: 5

vizkidd/QuickBLAST

BLAST without Sys.Call()

Language: C++ - Size: 7.56 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

amirfeizi/otargen

This is an R package to retrieve data from Open Target

Language: R - Size: 3.96 MB - Last synced at: 29 days ago - Pushed at: 6 months ago - Stars: 14 - Forks: 3

althonos/pyabricate

Pure Python port and interface to ABRicate, a tool for mass screening of contigs for antimicrobial resistance or virulence genes

Language: Python - Size: 24.4 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

LeafLight/SelectSpatialSpots

Select Spatial Spots Interactively

Language: Python - Size: 1.91 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

henrymwaka/sirna-selection-reslab Fork of whitehead/sirna

Modernized siRNA selection web platform – refactored for Ubuntu/nginx, reCAPTCHA-secured login, modular Perl CGI + PHP stack

Language: Perl - Size: 1.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

avrabyt/YouTube-Tutorials

📹 Collection of my Youtube Tutorials over the years! Read, write, and share what you create ✨🎈

Language: Python - Size: 701 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 118 - Forks: 48

taxburst/taxburst

sunburst plots for taxonomy - working to update Krona

Language: HTML - Size: 1.32 MB - Last synced at: 22 days ago - Pushed at: 4 months ago - Stars: 41 - Forks: 1

se7en69/CRC-DataLab

A tool for analyzing gene expression and genomic variants in colorectal cancer. It integrates pre-analyzed data, statistical analyses, machine learning, and text mining to provide actionable insights.

Language: Python - Size: 5.68 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

bcgsc/goldrush

Linear-time de novo Long Read Assembler

Language: C++ - Size: 4.27 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 41 - Forks: 2

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

raymondkiu/bioinformatics-tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files, rename fasta files (prefix and suffix) etc

Language: Shell - Size: 98.6 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 22 - Forks: 5

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

lcscs12345/riboss

Comparing translation of open reading frames within individual transcripts

Language: Python - Size: 262 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1

madsondeluna/procurator

Procurator is a Python command-line tool for analyzing prokaryotic DNA sequences in FASTA files. This work was developed as part of an assessment activity for the Computational Environments for Bioinformatics course at UFMG.

Language: Python - Size: 1.33 MB - Last synced at: 3 months ago - Pushed at: 3 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: 30 days ago - Pushed at: almost 2 years ago - Stars: 53 - Forks: 14

YaqiangCao/cLoops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

Language: Python - Size: 251 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 52 - Forks: 9

bcgsc/tigmint

⛓ Correct misassemblies using linked AND long reads

Language: Python - Size: 20.9 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 63 - Forks: 13

mt1022/gppy

[G]enomic [P]ositioning with [Py]thon

Language: Python - Size: 2.99 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 13 - Forks: 2

wjwei-handsome/ZeaGeneMap

A python tool for identifying the mapping of genes between two genomes.

Language: Python - Size: 374 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 0

RJWANGbioinfo/APAlyzer

APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is the comparison of sequencing reads in regions demarcated by high-quality polyadenylation sites (PASs) annotated in the PolyA_DB database (https://exon.apps.wistar.org/PolyA_DB/v3/). The current version (v3.0) uses RNA-seq data to examine APA events in 3’ untranslated regions (3’UTRs) and in introns. The coding regions are used for gene expression calculation.

Language: R - Size: 18.7 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 4

sebastianstupak/biolens-old-idea

Bioinformatics CLI tool for analysis and visualization

Language: Rust - Size: 764 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1

MatthiasZepper/thesis

My PhD thesis: Epigenetic characterization of murine Dnmt1-deficient MLL-AF9 leukemia

Language: TeX - Size: 46.5 MB - Last synced at: 7 days ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

johnnytam100/awesome-protein-design

A curated list of awesome protein design research, software and resources.

Size: 29.3 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 1

xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Language: Python - Size: 43.7 MB - Last synced at: 21 days ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 5

cliffren/scSurvival

scSurvival is a new tool for survival analysis from single cell cohort dataset.

Language: Jupyter Notebook - Size: 8.86 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ErickNavarroD/RAMEN

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

Language: R - Size: 13.4 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 5 - Forks: 0

mhtjsh/Bioinformatics_Algorithms

I am sharing my code repository to understand the working and principle of working of various BioInformatics code in Python

Language: Python - Size: 1.92 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 30 - Forks: 4

Sub-department-of-Genetics-ULSL/snp-analyser

🧬 A comprehensive bioinformatics tool for analyzing Single Nucleotide Polymorphisms (SNPs) and their effects on protein sequences with CLI and web interfaces.

Language: Python - Size: 27.3 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0