Search Results for "bioinformatics with python cookbook"
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Showing 61 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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Granite TSFM
Foundation Models for Time Series
...The repository focuses on end-to-end workflows: loading data, building datasets, fine-tuning forecasters, running evaluations, and serving models. It documents the currently supported Python versions and points users to where the core TSFM models are hosted and how to wire up service components. Issues and examples in the tracker illustrate common tasks such as slicing inference windows or using pipeline helpers that return pandas DataFrames, grounding the library in day-to-day time-series operations. The ecosystem around TSFM also includes a community cookbook of “recipes” that showcase capabilities and patterns. ... -
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AlphaFold 3
AlphaFold 3 inference pipeline
AlphaFold 3, developed by Google DeepMind, is an advanced deep learning system for predicting biomolecular structures and interactions with exceptional accuracy. This repository provides the complete inference pipeline for running AlphaFold 3, though access to the model parameters is restricted and must be obtained directly from Google under specific terms of use. The system is designed for scientific research applications in structural biology, biochemistry, and bioinformatics, enabling... -
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LLaMA Models
Utilities intended for use with Llama models
This repository serves as the central hub for the Llama foundation model family, consolidating model cards, licenses and use policies, and utilities that support inference and fine-tuning across releases. It ties together other stack components (like safety tooling and developer SDKs) and provides canonical references for model variants and their intended usage. The project’s issues and releases reflect an actively used coordination point for the ecosystem, where guidance, utilities, and... -
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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.... -
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A... -
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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... -
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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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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. -
Failed Payment Recovery for Subscription BusinessesFlexPay’s innovative platform uses multiple technologies to achieve the highest number of retained customers, resulting in reduced involuntary churn, longer life span after recovery, and higher revenue. Leading brands like LegalZoom, Hooked on Phonics, and ClinicSense trust FlexPay to recover failed payments, reduce churn, and increase customer lifetime value.
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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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PyArmadillo
linear algebra library for Python
PyArmadillo - streamlined linear algebra library for Python, with emphasis on ease of use. Alternative to NumPy / SciPy. * Main page: https://pyarma.sourceforge.io * Documentation: https://pyarma.sourceforge.io/docs.html * Bug reports: https://pyarma.sourceforge.io/faq.html * Git repo: https://gitlab.com/jason-rumengan/pyarma -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH... -
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TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and... -
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DeepLearning
Deep Learning (Flower Book) mathematical derivation
" Deep Learning " is the only comprehensive book in the field of deep learning. The full name is also called the Deep Learning AI Bible (Deep Learning) . It is edited by three world-renowned experts, Ian Goodfellow, Yoshua Bengio, and Aaron Courville. Includes linear algebra, probability theory, information theory, numerical optimization, and related content in machine learning. At the same time, it also introduces deep learning techniques used by practitioners in the industry, including... -
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Code Catalog in Python
Algorithms and data structures for review for coding interview
code-catalog-python serves as a grab-bag of small, readable Python examples that illustrate common algorithms, data structures, and utility patterns. Each snippet aims to be self-contained and easy to study, with clear inputs, outputs, and the essential logic on display. The catalog format lets you scan for an example, copy it, and adapt it to your use case without wading through a large framework. -
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BioSeq
A simple GUI for some of the biological sequence analysis.
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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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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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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,... -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
During the past few years, whole exome sequencing has imposed itself for genetic research, largely due to its use for detection of causative mutations responsible for Mendelian disorders. As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community,... -
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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). -
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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.
