zagrosman

I am an academic freelance researcher, working on natural products, protein-protein interactions, plant-microbiome interactions and playing with R codes :)

Iran

Pinned Repositories

biocode
Bioinformatics code libraries and scripts
Language:Python10
BioR
Herein, I'll try to develop R scripts for Biotechnologists who want to expand their idea easily.
Language:R1 1 00
chemminetools
ChemMine Tools: open source web framework for small molecule analysis
Language:JavaScript1 0 00
FastScript
This page will provide highly fast-running python scripts for biologists and biotechnologists. I want to develop my ideas to help my colleagues all over the world for saving their time during computational analyses.
Language:Jupyter Notebook53
fpocket-cavity-finder
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
Language:C10
MPBuilder
MPBuilder provides building capability for protein-detergent, bicelle, and lipid-scaffold (saposin nanoparticles, nanodiscs) complexes and links this to the ATSAS software package modules for model refinement and validation against the SAXS data.
Language:Python1 0 00
pteros
Modern and fast molecular analysis and modeling library for C++ and Python
Language:C++1 0 00
pymod
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Language:Python1 0 00
RNArtist
RNArtist allows you to design and paint your RNA 2D structures interactively. Coupled with the 3D viewer UCSF Chimera, use your 2D as a map to explore RNA 3D architectures.
Language:Kotlin10
Students
Free tools for biologists and biochemists
Language:Python61

zagrosman's Repositories

zagrosman/Students
Free tools for biologists and biochemists
Language:Python61
zagrosman/FastScript
This page will provide highly fast-running python scripts for biologists and biotechnologists. I want to develop my ideas to help my colleagues all over the world for saving their time during computational analyses.
Language:Jupyter Notebook53
zagrosman/BioR
Herein, I'll try to develop R scripts for Biotechnologists who want to expand their idea easily.
Language:R1 1 00
zagrosman/YouTubeTutorials-rnaseq-tutorial
11
zagrosman/Alignment
Language:Python
zagrosman/AutoDock-GPU
AutoDock for GPUs and other accelerators
Language:C++0 0
zagrosman/bigslice
A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
zagrosman/Coxpression-rnaseq-
A simple gene co-expression analyses workflow powered by tidyverse and graph analyses
zagrosman/DockingPie
A Consensus Docking Plugin for PyMOL
zagrosman/evomining
zagrosman/Finder
A fully automated gene annotator from RNA-Seq expression data
zagrosman/gapseq-pathway
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
zagrosman/genome_assembly_tools
List of genome assembly tools
zagrosman/ggalign
A 'ggplot2' Extension for Consistent Axis Alignment
zagrosman/ggExtra
📊 Add marginal histograms to ggplot2, and more ggplot2 enhancements
zagrosman/gh-actions-importer
GitHub Actions Importer helps you plan and automate the migration of Azure DevOps, CircleCI, GitLab, Jenkins, and Travis CI pipelines to GitHub Actions.
zagrosman/GMXvg
Plotting graphs from XVGs generated by GROMACS in Python
Language:Python0 0
zagrosman/gromacs
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
zagrosman/LiProS
zagrosman/MesquiteCore-Alignment
The core Mesquite repository for basic alignment
zagrosman/Molecular-Dynamics
Self explained tutorial for molecular dynamics simulation using gromacs
zagrosman/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
zagrosman/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
zagrosman/Pymol-script-repo
Collected scripts for Pymol
zagrosman/raxml-ngnewversion-phylogeny
RAxML Next Generation: faster, easier-to-use and more flexible
zagrosman/TCGAbiolinks
TCGAbiolinks
zagrosman/The-Economist
The_Economist经济学人
zagrosman/The-Python-Graph-Gallery
A website displaying hundreds of charts made with Python
zagrosman/VTX
Language:GLSL
zagrosman/zinc_downloader
Zinc Database Downloader & Merger