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245 search results found
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.
Galaxy
⭐
1,211
Data intensive science for everyone.
Khmer
⭐
729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Netprog_basics
⭐
682
Code, Examples, and Resources for the Network Programmability Basics Video Course
Chip Seq Analysis
⭐
586
ChIP-seq analysis notes from Ming Tang
Dnafeaturesviewer
⭐
500
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
Pyfaidx
⭐
427
Efficient pythonic random access to fasta subsequences
Nucleotide Transformer
⭐
305
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Whatshap
⭐
290
Read-based phasing of genomic variants, also called haplotype assembly
Prolif
⭐
286
Interaction Fingerprints for protein-ligand complexes and more
Dnaplotlib
⭐
238
DNA plotting library for Python
Lightdock
⭐
234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Pycoqc
⭐
213
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
Pyfastx
⭐
211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Nanoengineer
⭐
210
open-source nanotech CAD
Dnachisel
⭐
168
✏️ A versatile DNA sequence optimizer
Dne Dna Code
⭐
146
Provides code examples for DevNet Test Drive Catalyst (DNA) series
Pydna
⭐
140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Dna Seq Gatk Variant Calling
⭐
138
This Snakemake pipeline implements the GATK best-practices workflow
Chiron
⭐
114
A basecaller for Oxford Nanopore Technologies' sequencers
Lineage
⭐
114
tools for genetic genealogy and the analysis of consumer DNA test results
Ingan
⭐
111
Official code for the paper "InGAN: Capturing and Retargeting the DNA of a Natural Image"
Deepcpg
⭐
108
Deep neural networks for predicting CpG methylation
Optitype
⭐
106
Precision HLA typing from next-generation sequencing data
Buddysuite
⭐
105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Polyply_1.0
⭐
103
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Phageparser
⭐
101
A project to extract CRISPR information from open genetic data.
Bioblender
⭐
98
AddOn for Blender to do molecular work
Alv
⭐
95
A console-based alignment viewer
Deepmod
⭐
86
DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
Referenceseeker
⭐
85
Rapid determination of appropriate reference genomes.
Snps
⭐
82
tools for reading, writing, merging, and remapping SNPs
Rerio
⭐
80
Research release basecalling models and configurations
Animationdna
⭐
75
Maya > Arnold > Nuke pipeline
Arv
⭐
75
A fast 23andMe DNA parser and inferrer for Python
Made
⭐
72
MADE: Masked Autoencoder for Distribution Estimation
Dnac Templates
⭐
72
This site is aimed at helping with the adoption of Cisco Catalyst Center for Network Automation. Examples of Templates used in Cisco Catalyst Center with Velocity or Jinja2 Scripting, Variables, and Composite Approaches
Ttclust
⭐
68
clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
Pyfeat
⭐
68
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
Seqfold
⭐
66
nucleic acid folding
Dna Gan
⭐
64
DNA-GAN: Learning Disentangled Representations from Multi-Attribute Images
Dna Traits
⭐
64
A fast 23andMe genome text file parser, now superseded by arv
Catch
⭐
63
A package for designing compact and comprehensive capture probe sets.
Theta
⭐
62
Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
Dnacentersdk
⭐
61
Cisco DNA Center Python SDK
Kipoiseq
⭐
58
Standard set of data-loaders for training and making predictions for DNA sequence-based models.
Plasmid
⭐
53
web app to clone, edit in-place, and republish any web site
Atac Seq
⭐
51
Bioblender21
⭐
47
Blender plugin to process biological data and molecular work.
Cadnano2
⭐
45
Dfim
⭐
44
Deep Feature Interaction Maps (DFIM)
Dnacauldron
⭐
43
⚗️ Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies
Cfdnapattern
⭐
42
Pattern Recognition for Cell-free DNA
Dnapy
⭐
42
Code for DNA plasmid editing.
Partitionfinder
⭐
42
PartitionFinder discovers optimal partitioning schemes for DNA sequences.
Circle Map
⭐
39
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
Genomelake
⭐
37
Simple and efficient access to genomic data for deep learning models.
Mapdamage
⭐
37
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Dnac Aura
⭐
36
Dnamatch Tools
⭐
35
open source tools providing capabilities for your DNA data from various DNA testing companies
Cadnano2
⭐
35
Cadnano2
Data_science_in_biology
⭐
35
projects using galaxy, python, linux command line to analyze sequencing data
Strangervisions
⭐
35
Oxdna
⭐
32
A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
Genetic Trait Detector
⭐
30
This python script detects known traits in raw human genetic data.
Linkview
⭐
30
DNA序列比对结果 可视化展示工具
Coral
⭐
29
Coral, a library and framework for specifying synthetic biology design processes.
Cpgtools
⭐
29
Python package to analyze DNA methylation data
Sccaller
⭐
28
Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
Sequenticon
⭐
28
👾 Generate identicons for DNA sequences with Python
Hierarchical Clustering
⭐
27
A Python implementation of divisive and hierarchical clustering algorithms. The algorithms were tested on the Human Gene DNA Sequence dataset and dendrograms were plotted.
Candis
⭐
27
🎀 A data mining suite for gene expression data.
Nucdiff
⭐
27
In-depth characterization and annotation of differences between two sets of DNA sequences
Radia
⭐
27
RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
Geneblocks
⭐
27
💠 Find common blocks and differences between DNA sequences
Nanomod
⭐
26
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
Primavera
⭐
25
🌸 Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.
Simdna
⭐
25
A python library for creating simulated regulatory DNA sequences
Orfipy
⭐
25
Fast and flexible ORF finder
Dna
⭐
23
A python script to encode/decode arbitrary computer files into DNA sequences.
Gembs
⭐
23
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
Bamgineer
⭐
22
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Rosalind
⭐
22
Rosalind Bioinformatics Problems
Crazydoc
⭐
22
Read DNA sequences from colourful Microsoft Word documents
Dnaweaver
⭐
22
A route planner for DNA assembly
Dna Bot
⭐
22
Sequencework
⭐
22
programs and scripts, mainly python, for analyses related to nucleic or protein sequences
Dna Sculpture
⭐
21
3D printed sculpture of a DNA molecule, showing my own genome
Mbin
⭐
21
mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
Barcodefinder
⭐
20
all-in-one solution for discovering novel DNA barcode
Phasefinder
⭐
20
A pipeline to computationally identify invertible DNA regions and quantify their orientations.
Sctools
⭐
20
Utilities for large scale distributed single cell data processing
Getmydnamatches
⭐
20
Noisecancellingrepeatfinder
⭐
19
Noise-Cancelling Repeat Finder
Flu Prediction
⭐
18
Predicting Future Influenza Virus Sequences with Machine Learning
Polygonpainter
⭐
18
Freebarcodes
⭐
18
FREE Divergence Error-Correcting DNA Barcodes
Awesome Cisco Dnac
⭐
18
A curated list of awesome Cisco DNA Center frameworks, libraries, sdk, sample codes and resources
Circdna
⭐
18
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
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