Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for python bioinformatics
bioinformatics
x
python
x
1,035 search results found
Dash
⭐
19,976
Data Apps & Dashboards for Python. No JavaScript Required.
Biopython
⭐
3,918
Official git repository for Biopython (originally converted from CVS)
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Awesome Single Cell
⭐
2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Scanpy
⭐
1,729
Single-cell analysis in Python. Scales to >1M cells.
Galaxy
⭐
1,211
Data intensive science for everyone.
Multiqc
⭐
1,159
Aggregate results from bioinformatics analyses across many samples into a single report.
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Deep_gcns_torch
⭐
940
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
Graphein
⭐
932
Protein Graph Library
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Ncbi Genome Download
⭐
784
Scripts to download genomes from the NCBI FTP servers
Khmer
⭐
729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Deeptools
⭐
644
Tools to process and analyze deep sequencing data.
Seq
⭐
624
A high-performance, Pythonic language for bioinformatics
Plantcv
⭐
590
Plant phenotyping with image analysis
Awesome
⭐
565
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
Bcbb
⭐
565
Incubator for useful bioinformatics code, primarily in Python and R
Biostar Central
⭐
563
Biostar Q&A
Dgl Lifesci
⭐
558
Python package for graph neural networks in chemistry and biology
Dash Cytoscape
⭐
555
Interactive network visualization in Python and Dash, powered by Cytoscape.js
Grakel
⭐
540
A scikit-learn compatible library for graph kernels
Biotite
⭐
515
A comprehensive library for computational molecular biology
Dnafeaturesviewer
⭐
500
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
Dash Bio
⭐
485
Open-source bioinformatics components for Dash
Sniffles
⭐
479
Structural variation caller using third generation sequencing
Pycirclize
⭐
476
Circular visualization in Python (Circos Plot, Chord Diagram)
Cutadapt
⭐
475
Cutadapt removes adapter sequences from sequencing reads
Pydeseq2
⭐
470
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Redun
⭐
464
Yet another redundant workflow engine
Clinker
⭐
452
Gene cluster comparison figure generator
Sourmash
⭐
431
Quickly search, compare, and analyze genomic and metagenomic data sets.
Biocode
⭐
430
Bioinformatics code libraries and scripts
Pyfaidx
⭐
427
Efficient pythonic random access to fasta subsequences
Edlib
⭐
421
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Cobrapy
⭐
414
COBRApy is a package for constraint-based modeling of metabolic networks.
Anvio
⭐
396
An analysis and visualization platform for 'omics data
Gtdbtk
⭐
383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Bakta
⭐
365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Arvados
⭐
354
An open source platform for managing and analyzing biomedical big data
Bioconvert
⭐
344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Plip
⭐
320
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
Pdb Tools
⭐
319
A dependency-free cross-platform swiss army knife for PDB files.
Histolab
⭐
315
Library for Digital Pathology Image Processing
Bds Files
⭐
305
Supplementary files for my book, "Bioinformatics Data Skills"
Glue
⭐
294
Graph-linked unified embedding for single-cell multi-omics data integration
Pybedtools
⭐
286
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Dance
⭐
284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
Canvasxpress
⭐
282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Cellrank
⭐
279
CellRank: dynamics from multi-view single-cell data
Pysradb
⭐
269
Package for fetching metadata and downloading data from SRA/ENA/GEO
Genometools
⭐
261
GenomeTools genome analysis system.
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Lightdock
⭐
234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Intermine
⭐
228
A powerful open source data warehouse system
Hgvs
⭐
226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Parallel Fastq Dump
⭐
224
parallel fastq-dump wrapper
Sortmerna
⭐
220
SortMeRNA: next-generation sequence filtering and alignment tool
Scgen
⭐
215
Single cell perturbation prediction
Pronto
⭐
212
A Python frontend to (Open Biomedical) Ontologies.
Pyfastx
⭐
211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Tools
⭐
205
Python package with helper tools for the nf-core community.
Drep
⭐
199
Rapid comparison and dereplication of genomes
Hicexplorer
⭐
197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Circlator
⭐
193
A tool to circularize genome assemblies
Ppanggolin
⭐
191
Build a partitioned pangenome graph from microbial genomes
Deepecg
⭐
187
ECG classification programs based on ML/DL methods
Bioinformatics With Python Cookbook Second Edition
⭐
184
Bioinformatics with Python Cookbook Second Edition, published by Packt
Cooler
⭐
183
A cool place to store your Hi-C
Pycomplexheatmap
⭐
182
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Deepconsensus
⭐
180
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Pygenomeviz
⭐
177
A genome visualization python package for comparative genomics
Dnachisel
⭐
168
✏️ A versatile DNA sequence optimizer
Tobias
⭐
162
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Biocypher
⭐
160
A unifying framework for biomedical research knowledge graphs
Insilicoseq
⭐
158
🚀 A sequencing simulator
Afterqc
⭐
157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Diffxpy
⭐
157
Differential expression analysis for single-cell RNA-seq data.
Antismash
⭐
155
antiSMASH
Metagem
⭐
155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Indra
⭐
154
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Readfish
⭐
152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
Proteinflow
⭐
151
Versatile computational pipeline for processing protein structure data for deep learning applications.
Pymzml
⭐
151
pymzML - an interface between Python and mzML Mass spectrometry Files
Bioinformatics Workflows
⭐
151
minimal example implementations for bioinformatics workflow managers
Gatk Sv
⭐
148
A structural variation pipeline for short-read sequencing
Clairvoyante
⭐
142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Pydna
⭐
140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Obofoundry.github.io
⭐
140
Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
Pyani
⭐
140
Application and Python module for average nucleotide identity analyses of microbes.
Ariba
⭐
135
Antimicrobial Resistance Identification By Assembly
Souporcell
⭐
134
Clustering scRNAseq by genotypes
Gubbins
⭐
133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Sigprofilerextractor
⭐
132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Seq2science
⭐
132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Compleasm
⭐
132
A genome completeness evaluation tool based on miniprot
Snakefmt
⭐
131
The uncompromising Snakemake code formatter
Tskit
⭐
131
Population-scale genomics
Rna Tools
⭐
129
🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
Related Searches
Python Flask (17,643)
Python Docker (14,113)
Python Machine Learning (14,099)
Python Tensorflow (13,736)
Python Command Line (13,351)
Python Deep Learning (13,092)
Python Jupyter Notebook (12,976)
Python Network (11,495)
Python Testing (9,479)
Python Natural Language Processing (9,064)
1-100 of 1,035 search results
Next >
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.