Search Results for "program files"
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Showing 43 open source projects for "program files"
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1
Jmol
An interactive viewer for three-dimensional chemical structures.
...Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. ... -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
...Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
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MPIGeneNet
Parallel tool to construct gene co-expression networks
...This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch the application once) and avoids writing/reading from intermediate files among the modules. -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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Lipid Reporter
Modifies csv files with a range of user defined filters.
** Updated for Windows 10** Lipid Reporter takes your plain old Progenesis QI search exports and allows you to manipulate them in a quick, safe, predictable way. Now with better support for Progenesis QI grouped output! Why muddle things up with Excel? Use Lipid Reporter instead. The supplied filters are all about Lipids. Add the category names, reject Ids that our outside of your favourite retention time range and lots more! This program is not produced by Nonlinear Dynamics... -
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
...Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be downloaded here: https://sourceforge.net/p/genform/code/HEAD/tree/trunk/data/ A first program call could look like this: GenForm ms=SinapinicAcidMs.txt msms=SinapinicAcidMsMs.txt exist out -
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
...The Metacharcter and their behaviours in the context of regular expressions are the main methods to identify the different searched patterns and by different combination of Metacharcter, the programmed tool can search and detect the pattern of DNA sequence. Repeater Finder Regular Expression Tool Regular Expression for Protein Motif Search and SSR sequence. https://sourceforge.net/projects/rfret/files/RFRE122019.exe/download https://www.preprints.org/manuscript/201910.0249/v1 https://sites.google.com/must.edu.eg/finding-dna-repeats/home ---------------------------------------------- *****Very important program must be downloaded before you run the EXE FILE OF RFRE***** 1-VB6 Runtime Plus 2.2.exe , https://sourceforge.net/projects/vb6extendedruntime/ -
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
...Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for rasterization, or used in page design software like Illustrator. -
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10
JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). 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/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. -
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cdfread is a program for people wirking with mass spectrometry datasets. cdfread implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format. Centroid and profile data are supported.
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MGFVisor
Visor for mass spectrometry MGF files
Visor for mass spectrometry MGF files (Python 3 version). 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/mgfvisor3/code/ci/default/tree/README.md -
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FastaTools
Performs several operations to Fasta protein databases
FastaTools performs several operations to Fasta protein databases. 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/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M.,... -
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bwfinder
Exogenous feature extractor from brainwaves
This program should detect strong external signals in brainwave recordings. Weak signals are not detected. This program requires the "edf2ascii" utility, a set of EDF files with brainwave recordings in the "EDF/" directory and two empty destination directories named "founds/" and "losts/". This is my first Matlab/Scilab program, apologies for the poor style but Scilab lacks and bugs prevent the writing of a pure code. -
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MGF 2 FOR-JSON
Conversion of MGF files to JSON format
Want to convert an MGF file to JSON format? This is the app for you, especially if you want to use the JSON file in the FOR-IDENT search program. If you don't know what MGF file, JSON format, FOR-IDENT search program is then this isn't the app for you. Happy conversion! -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
...MSTgold accepts single-character data that are nucleotides, amino acids, binary characters, or SNPs; integers that represent, for instance, the lengths of VNTRs or microsatellites; and distance matrices. The MSTgold package includes Mac OS X, Linux, and Windows executables of the MSTgold program, a detailed Manual, example data and results, and executables of the program Fasta2MSTG which converts Fasta sequence files to the MSTgold input format. -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. 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. -
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VCF Explorer
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Efficient memory management of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. ... -
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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... -
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denovo_hit
Outputs potential denovo variants from VCF given pedigree information.
Program takes variants calls and determines if the call is novel for a child compared to parents. Program can handle both annotated and unannotated VCF files, however output file is not compatible with GATK's snpEff, so you should annotate prior to using denovo_hit. Usage: ./denovo_hit <VCF file> <PED file> Output: ./potential_denovo.txt To compile: g++ -std=c++11 denovo_hit.cpp -o denovo_hit Please see files for example VCF file, and pedigree file. ... -
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...ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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Visual Blast
GUI to accelerate protein and nucleotide BLAST analysis
BLAST (Basic Local Alignment Search Tool) is a popular program that retrieves a library of sequences that resemble the query. The major problem experienced by new users of BLAST revolves around constructing syntactically and semantically correct command line, getting input files into acceptable formats and assessing the output. Visual BLAST is a Graphical User Interface written in C# and it was developed to simplify the parameters setting for BLAST searches. -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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miRStat
identification of common sets of microRNAs for groups of genes
miRStat enables identification of regulatory microRNA targeting several genes in a custom gene group. This Python application is based on the TargetScan 6.2 microRNA target prediction data. Conserved and Nonconserved site context+ scores files are required (unzip and place to directory with program). Available at http://targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61
