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86 search results found

Lightdock ⭐ 234

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

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

Rnalysis ⭐ 114

RNA sequencing analysis software

Abricate ⭐ 109

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Youtube Tutorials ⭐ 100

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

Open Cravat ⭐ 98

A modular annotation tool for genomic variants

🚀 seqfu - Sequece Fastx Utilities

Rna Bloom ⭐ 66

🌺 reference-free transcriptome assembly for short and long reads

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Snakecharm ⭐ 58

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

Ilearnplus ⭐ 57

iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

⛓ Correct misassemblies using linked AND long reads

Geneview ⭐ 51

Genomics data visualization in Python by using matplotlib.

Metacache ⭐ 49

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

Htstream ⭐ 48

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

Bioblender21 ⭐ 47

Blender plugin to process biological data and molecular work.

Scissor package

Fluentdna ⭐ 43

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Webservice Clients ⭐ 43

A collection of Web Service Clients to consume EBI's tools via REST and SOAP APIs.

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

Covtobed ⭐ 36

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

Localpdb ⭐ 36

Python package to manage protein structures and their annotations

Annotation helper tool for the manual curation of transposable element consensus sequences

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

counts k-mers, written in rust

Speciesprimer ⭐ 26

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

Goldrush ⭐ 26

Linear-time de novo Long Read Assembler

Methphaser ⭐ 24

MethPhaser: methylation-based haplotype phasing of human genomes

Biodiscml ⭐ 23

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

an implementation of NSGA-II in java

Sumstatsrehab ⭐ 20

GWAS summary statistics files QC tool

Kgwasflow ⭐ 19

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

Reactomepy ⭐ 19

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

PENCIL is a novel tool for singlecell data analysis to identify phenotype associated subpopulations and informative genes simultaneously.

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

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

⛓️ Construct a Physical Map from Linked Reads

MView extracts and reformats the results of a sequence database search or multiple alignment.

Deepcoil ⭐ 16

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

Te_finder ⭐ 16

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

Bioinformatics Tools ⭐ 14

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

Viola Sv ⭐ 14

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.

Biosmalltalk ⭐ 14

Bioinformatics Library for Pharo

Genegrouper ⭐ 13

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

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

Fingernat ⭐ 12

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

Make phylogenetic trees and lineages from the NCBI Taxonomy database

Meshclust2 ⭐ 11

MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences

Mobidetails ⭐ 11

WebApp for DNA variants interpretation

Exploring Isoform-specific interactions

Webservice Cwl ⭐ 10

Programmatic access to various data resources and analysis EBI tools via CWL

Guidescan Cli ⭐ 10

A gRNA database generation tool.

Kmercamel ⭐ 9

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

Track single cells and profile the cell cycle with PCNA fluorescence images

Python Library for data analysis based on GMQL

Practical Optical Tweezers Analysis TOol

Embeddings to Network Alignment - align biological networks between two species

fast and comprehensive k-mer counting package

A software to detect virome-wide integrations

A web templating engine for visualizing and sharing life science datasets

Hichip_peaks ⭐ 7

A tool to analyse HiChIP data

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

A network-based approach for exon set enrichment

MHC class II binding prediction

Cyclobranch ⭐ 7

A tool for mass spectrometry data analysis.

🧬 This is a toolkit to handle bio-data from WeiBin Lab

CNV analysis based on the depth of coverage of Illumina data

Guidescan Web ⭐ 6

A guideRNA design tool for the modern era.

Tisigner Reactjs ⭐ 6

TISIGNER: Unleash the power of synthetic biology

Fast sequence vectorization for metagenomics analysis. Converts input sequences into oligonucleotide frequency vectors, fast!

Hlaclustrview ⭐ 6

R package specialized in HLA typing clustering and visualization based on specific similarity metrics

A SNP-aware short read aligner

Ciara_python ⭐ 6

Implementation of entropy of mixing algorithm in python

Pysigprofiler ⭐ 6

Python implementation of SigProfiler

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

Spatial Live ⭐ 6

A Lightweight & Versatile Visualization Tool for Spatial-Omics Data

🌊 Analyse experimental conditions and replicates jointly to remove cell-type specific bias in multi-condition ChIP-Seq

Fast and Accurate Approach of Structural Variations Detection for Short DNA fragments

Ribo Oddr ⭐ 5

Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

Lofreq Fpga ⭐ 5

FPGA Acceleration for the LoFreq variant caller

a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.

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

1-86 of 86 search results

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