Search Results for "file analysis"
Sort By:
Showing 76 open source projects for "file analysis"
View related business solutions-
Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
-
Compliant and Reliable File Transfers Backed by Top Security CertificationsStop relying on non-certified, legacy file transfer tools that creak under the weight of modern security demands. Get full audit trails, advanced access controls and more supported by an award-winning team of experts. Start your free 25-day trial today.
-
1
iCn3D
Web-based protein structure viewer and analysis tool
...View a 3D structure in iCn3D, input a PDB ID, and click "Load". You can also click the "File" menu to "Open File" or input other IDs. You can open a browser in your Virtual Reality (VR) headset and view a 3D structure in iCn3D. Then click the button "Enter VR" at the bottom center of your browser to enter the VR view. You can select residues with the trigger button. -
2
Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. -
3
PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes... -
4
mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
-
$300 Free Credits to Build on Google CloudStart your next project with $300 in free Google Cloud credit. Spin up VMs, run containers, query petabytes in BigQuery, or build agents with Gemini Enterprise Agent Platform. Once your credits are used, keep building with 20+ always-free tier products including Compute Engine, Cloud Storage, GKE, and Cloud Run functions. No commitment required—just sign up and start building.
-
5
ProStack
ProStack - a platform for image processing and analysis
ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio -
6
GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure... -
7
MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In 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 -... -
8
SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
9
QUAST
Quality Assessment Tool for Genome Assemblies
...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 comprehensive analysis results in summary tables (in plain text, tab-separated, and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research. -
Forever Free Full-Stack Observability | Grafana CloudBuilt on open standards like Prometheus and OpenTelemetry, Grafana Cloud includes Kubernetes Monitoring, Application Observability, Incident Response, plus the AI-powered Grafana Assistant. Get started with our generous free tier today.
-
10
PlateEditor
PlateEditor, a free web application to work with multi-well plates
PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this... -
11
CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. -
12
uac19
Analyze COVID-19 csv files
A flexible command line tool to analyze COVID-19 csv files https://github.com/nytimes/covid-19-data https://ourworldindata.org/coronavirus-source-data The rpm build is rh7 the tgz installs on Windows cygwin. -
13
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... -
14
ECOLOG
A database management system for ecological field surveys
ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories. The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics,... -
15
MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
16
MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS 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 variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php -
17
Palibino
Pascal library for bioinformatics
Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology. -
18
gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
...You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
19
Python4Proteomics Course
Python course for Proteomics analysis
Python course (in Spanish) for Proteomics analysis using basically Jupyter NoteBooks. For more information, you can have a look at the readme.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/p4p/code/ci/default/tree/readme.md -
20
NOVA
Analysis and visualization of complexome profiling data.
...Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441 -
21
Patlac--Xml2cpp is a totally customizable code generator that generates classes (c++ for now) automatically from a xsd schema. Classes are described in google-ctemplate files and a xml options file allow precise definition of projects.
-
22
The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
-
23
D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of... -
24
lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
25
fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by...