Search Results for "bio-bwa" - Page 8
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Showing 3101 open source projects for "bio-bwa"
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We design our technology to make workforce management easier. APS offers core HR, payroll, benefits administration, attendance, recruiting, employee onboarding, and more.
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QUANTUM SALIS
Statistical algorithms for life sciences
Collection of algorithms for computational statistics in life sciences -
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Genome Information Entropy Spectrum
A code that computes information entropy spectrum of any genome.
We request users of this software to please kindly cite this article: Melvin M. Vopson, Samuel C. Robson, A new method to study genome mutations using the information entropy, Physica A: Statistical Mechanics and its Applications, Volume 584, 126383 (2021) https://doi.org/10.1016/j.physa.2021.126383 The GENIES program is a stand alone code, with an easy to use graphical interface that performs the following tasks: a) it loads up two genome files (original and mutated); b) it computes... -
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Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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viRome
R code/package for virus small RNA sequence data
Please use code here: https://github.com/mw55309/viRome_legacy -
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VMS Draw
user-friendly access to the latest computational spectroscopy tools
VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set... -
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SMTracker (v1.5, v2.0)
A tool for analysis and visualization of single-molecule tracking data
SMTracker v2.0 is a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualising and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by- track basis. Diffusion parameters and motion behaviour is analysed by several methods: a) by a Gaussian mixture model ,or b) by using the cumulative probability distribution of square displacements, c) Mean-Squared... -
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MSP Builder 2
Converts text files (such as csv, tsv, txt) to MSP files
Take a list from a search and how do you use that as a search. Answer: As an MSP file. But how do you make one? Answer: With this app. Convert your csv etc files to MSP. You define the relationship (the mapping) and take it from there. Includes a couple of examples. -
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The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.
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Evolia is a web and mobile platform that connects enterprises with 1000’s of local shift workers and offers free workforce scheduling and time and attendance solutions. Is your business on Evolia?
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QuantifyPoly(A)
Quantification of poly(A) sites from 3' end sequencing data
QuantifyPoly(A) - a tool for quantification of poly(A) sites from 3' end sequencing data. [1] QuantifyPoly(A) user manual Please visit the Wiki page of this website. [2] QuantifyPoly(A) Q&A For Q&A, please visit the Blog page of this website. [3] QuantifyPoly(A) bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. -
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Cell Paint
cellPAINT allows users to create living illustrations of biology.
cellPAINT is a free-form painting app that allows users to create their own living illustrations of cellular landscapes. There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is... -
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Tempomat
Tools for analysis of biological time series
Tempomat is software that supports statistical analysis of time series in the life sciences. -
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be... -
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from... -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated... -
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SPIRE
A tool to compute projections of membrane structures
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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exome-test
script for variant calling of Exome-Seq
exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error... -
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geostd is an open-source set of restraints for molecules involved in macromolecular structure refinement. The restraints reduce the number of variables making the solution of protein structures a more tractable process.
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slimfastq
An efficient lossless compression for fastq files.
slimfastq is a cli application that compresses/decompresses fastq files. It features: * High compression ratio * Relatively low cpu/memory usage * Truly lossless compression/decompression -
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Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing 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... -
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miRprimer
Automatic design of primers for miR-specific RT-qPCR
miRprimer designs primers for PCR amplification of microRNAs as described (Busk (2014). A tool for design of primers for microRNA-specific quantitative RT-qPCR. BMC Bioinformatics. 15, 29) for use with the method miR-specific RT-qPCR (Cirera, S., and Busk, P.K. (2014). Quantification of miRNAs by a simple and specific qPCR method. Methods in Molecular Biology. 1182, 73-81.). The program was written in Ruby and is available as source code for developers and as an .exe file for easy use.