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Showing 51 open source projects for "scripts"
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code" button. ... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
... - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more - Software Authorship - Muzammil Kabier -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred... -
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dataMAPPs
R based pipeline for MHC-associated peptide proteomics (MAPPs) data
...It features quality control of the raw data, across-sample/across-donor normalization and visualization of results in a heatmap style (heatMAPPs). dataMAPPs' core is a generic R library that can be tailored to specific projects via dedicated control scripts which also allow reproducible recalculation of results. Consult README file for installation and usage instructions. Further documentation is supplied in PDF format. dataMAPPs is published under GPL license by a team of scientists working for Hoffmann-La Roche AG in Basel, Switzerland. The software is provided as is, to hopefully benefit other researchers. ... -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually. -
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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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BEMoDA
Dissolution profile comparison Model Dependent-Independent Approach
Dissolution profile comparison (Biowaiver aid) Model Dependent-Independent Approach scripts for in-vitro dissolution profile comparison as proposed by Sathe et al. in 1996 (Sathe PM, Tsong Y, Shah VP. In-vitro dissolution profile comparison: statistics and analysis, model dependent approach. Pharm Res. 1996 Dec;13(12):1799-803) and Tsong et al. in 1996 (Tsong Y, Hammerstrom T, Sathe P, Shah VP. (1996) Statistical Assessment of Mean Differences between Two Dissolution Data Sets, Drug Info. ... -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
...There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation script languages such as Awk and Perl are available, and many users, uses these to do their works. However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. ... -
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scFvMiner
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. ... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. ... -
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Cloudomics-for-AWS
AWS resources for Bioinformatics Workflows & Apps
Library of scripts used for authenticating researchers who submit bioinformatics datasets to an S3 bucket for analytics using AWS resources (Development start : 2015 as part of Cloudomics, formally www.mycloudomics.com) -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. -
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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 variation, and expression datasets is now available. ... -
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Lab Processes
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Lab Processes. We want to hear your feedback! Request new Lab Processes feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/lp Lab Processes is a comprehensive and straightforward application specially designed for biologists and chemists who need to conduct a wide variety of tests and experiments on animals. Lab Processes requires minimal computing skills. Genetic and physiological data can be entered either... -
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budden2015treeome
Scripts and supplementary data for budden2015treeome manuscript
Scripts and supplementary data for the manuscript "Modelling the conditional regulatory activity of methylated and bivalent promoters" -
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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems.
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budden2014predictive
Scripts and supplementary data for budden2014predictive manuscript
Scripts and supplementary data for the manuscript "Predictive modeling of gene expression from transcriptional regulatory elements" -
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
The SeqSelector toolset is a suite of user-friendly, platform independent python scripts to facilitate selection of sequences for targeted enrichment of next-generation libraries through hybridization-based sequence capture. The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. ... -
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AbMining ToolBox
python scripts to analyze antibody libraries
02-14-2014. Hamming distance calculation has been updated. These are python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq) as described in D'Angelo et al MAbs. 2014 Jan 1;6(1):160-72. -
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A Perl module and selection of scripts to aid processing of NEXUS-based tree files ready for supertree construction in programs like PAUP*.
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PolyCTLDesigner
Python scripts for designing polyepitope T-cell immunogens
Given the peptides (T-cell epitopes) PolyCTLDesigner selects flanking sequences to optimize TAP-binding and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing and minimizing the number of junctional epitopes. For constructing polyepitopes PolyCTLDesigner utilizes known amino acid patterns of proteasome cleavage and TAP-binding specificity. PolyCTLDesigner is also able to choose... -
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CoVEC
Consensus Variant Effect Classification
The package provides SVM models to be used with SVMlight (http://svmlight.joachims.org/) for drawing a consensus out of individual 3rd-party predictions about the effect of mutations. The 3rd party tools are SIFT, Polyphen2, SNPs&GO and Mutation Assessor. The package also provides a series of Perl modules and scripts to assist in the preparation of data. The modules can be used to build custom tools and pipelines, whereas the scripts provide basic executable implementations based on the modules. SVMlight, SIFT, Polyphen2, SNPs&GO and Mutation Assessor are the property of their respective authors and institutions and are not distributed in this package. -
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...Have a look at the readme file when you download your new copy from https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/ Make also sure to have a look at https://sourceforge.net/projects/rawgeno/files/ where you can find a detailed manual, demo datasets and many demo scripts.
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Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
The purpose of DressUp is to create an end-to-end RNA seq pipeline in which all of the steps of analyzing data from an Illumina sequencer is done in one step in an HPC environment. RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs...
