Search Results for "base-files"
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14 programs for "base-files" with 2 filters applied:
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop... -
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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.
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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... -
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RNAfdl
RNA force directed layout
RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings. -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A... -
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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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fast_count_multi
Extremely fast NGS read counter
Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. usage ./fast_count_multi num_threads... -
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A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
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SWATnalysis
Analysis of SWAT output files
Runs the Soil and Water assessment Tool (SWAT), and analyzes associated output files. Converts archaically formatted SWAT output files into more user friendly excel csv files, performs graphical analysis, calculates area weighted precipitation values, and performs statistical analysis of observed data versus simulated data. -
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ViNSS View
Vienna Notation Secondary Structure Viewer
ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing. -
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DeNovoCheck
DeNovoCheck: Inheritance analysis for NGS trio data
DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. -
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bint
Converts intensity text files to binary for fast subsetting
bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file... -
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EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use. On modern computers, DOS software can run in DOSBOX (https...
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