Search Results for "bioinformatics with python cookbook"
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Showing 50 open source projects for "bioinformatics with python cookbook"
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Llama Cookbook
Solve end to end problems using Llama model family
The Llama Cookbook is the official Meta LLaMA guide for inference, fine‑tuning, RAG, and multi-step use-cases. It offers recipes, code samples, and integration examples across provider platforms (WhatsApp, SQL, long context workflows), enabling developers to quickly harness LLaMA models -
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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
AWS ParallelCluster is an AWS supported Open Source cluster management tool that makes it easy for you to deploy and manage High Performance Computing (HPC) clusters in the AWS cloud. Built on the Open Source CfnCluster project, AWS ParallelCluster enables you to quickly build an HPC compute environment in AWS. It automatically sets up the required compute resources and a shared filesystem and offers a variety of batch schedulers such as AWS Batch and Slurm. AWS ParallelCluster facilitates... -
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Codon
A high-performance, zero-overhead, extensible Python compiler
Codon is a high-performance Python compiler that compiles Python code to native machine code without any runtime overhead. Typical speedups over Python are on the order of 100x or more, on a single thread. Codon supports native multithreading which can lead to speedups many times higher still. The Codon framework is fully modular and extensible, allowing for the seamless integration of new modules, compiler optimizations, domain-specific languages and so on. We actively develop Codon extensions... -
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audioFlux
A library for audio and music analysis, feature extraction
A library for audio and music analysis, and feature extraction. Can be used for deep learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. audioflux is a deep learning tool library for audio and music analysis, feature extraction. It supports dozens of time-frequency analysis transformation methods and hundreds of corresponding time-domain and frequency-domain feature combinations. It can be provided to deep learning networks for training and is used... -
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DGL
Python package built to ease deep learning on graph
Build your models with PyTorch, TensorFlow or Apache MXNet. Fast and memory-efficient message passing primitives for training Graph Neural Networks. Scale to giant graphs via multi-GPU acceleration and distributed training infrastructure. DGL empowers a variety of domain-specific projects including DGL-KE for learning large-scale knowledge graph embeddings, DGL-LifeSci for bioinformatics and cheminformatics, and many others. We are keen to bringing graphs closer to deep learning researchers. We... -
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Armadillo
fast C++ library for linear algebra & scientific computing
* Fast C++ library for linear algebra (matrix maths) and scientific computing * Easy to use functions and syntax, deliberately similar to Matlab / Octave * Uses template meta-programming techniques to increase efficiency * Provides user-friendly wrappers for OpenBLAS, Intel MKL, LAPACK, ATLAS, ARPACK, SuperLU and FFTW libraries * Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. * Downloads: http://arma.sourceforge.net... -
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LaTeX Cookbook
A comprehensive LaTeX template with examples for theses, books, etc.
This repo contains a LaTeX document, usable as a cookbook (different "recipes" to achieve various things in LaTeX) as well as a template. The resulting PDF covers LaTeX-specific topics and instructions on compiling the LaTeX source. -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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DataPrep
Python-based data preprocessing tool
DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal strategies... -
Picsart Enterprise Background Removal API for Stunning eCommerce VisualsWith our Remove Background API tool, you can access the transformative capabilities of automation , which will allow you to turn any photo asset into compelling product imagery. With elevated visuals quality on your digital platforms, you can captivate your audience, and therefore achieve higher engagement and sales.
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Code Cookbook
Reusable code patterns which you can use as reference or copy
Reusable code patterns which you can use as reference or copy to your project. Achieve small or large tasks using recipes that contain steps, scripts, and config files. -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome... -
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DeepLearning
Deep Learning (Flower Book) mathematical derivation
... feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling and practical methods, and investigates topics such as natural language processing, Applications in speech recognition, computer vision, online recommender systems, bioinformatics, and video games. Finally, the Deep Learning book provides research directions covering theoretical topics including linear factor models, autoencoders, representation learning, structured probabilistic models, etc. -
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Python Cookbook
Python Cookbook, 3rd edition translation
Translators have always insisted on using Python 3 because it represents the future of Python. Although backward compatibility is its flaw, this situation will change sooner or later, and the future of Python 3 needs everyone's help and support. At present, most of the tutorial books on the market and online manuals are basically 2.x series, and there are few books based on 3.x series. "Python Cookbook" 3rd Edition, which is completely based on Python 3, is a very well written book... -
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BioSeq
A simple GUI for some of the biological sequence analysis.
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Pipebar
A fast and accurate pipeline for DNA barcoding analysis.
Molecular analyses require the use of multiple bioinformatics tools. Here we proposed a pipeline for DNA chromatograms analysis of Sanger platform by open-source tools integration in order to reduce cost with standard commercial licences ensuring high quality, robustness with reduced time. Pipebar is a python application created to automatization of processing chromatogram trace files to high-quality DNA sequences for downstream analyses. -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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AmpliMethProfiler
CpG methylation analysis of amplicons from bisulfite sequencing
ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. Specifically, ampliMethProfiler provides an easy and user friendly way to extract and analyze the epiallelic composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and QIIME tools. It can be run on Linux and OS X... -
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Scaffold_Builder
Combining de novo and reference-guided assembly with Scaffold_builder
Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps. (c) Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA. Please... -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence... -
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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). Publication to be cited: Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools... -
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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MicrobeGPS
The Explorative Taxonomic Profiling Tool for Metagenomic Data
MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily. -
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fitGCP
Fitting genome coverage distributions with mixture models
... this information accessible can improve the quality of sequencing experiments and quantitative analyses. fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Please find the accompanying paper here: http://dx.doi.org/10.1093/bioinformatics/btt147 -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices...
