Search Results for "bio-bwa" - Page 13
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1339 programs for "bio-bwa" with 1 filter applied:
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An implementation of the Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method for MATLAB and R. The supplied functionality includes e.g. cross-validation, kernel parameter optimization, model diagnostics and plot tools.
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Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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Pugsly
Command-line, PubChem PUG client, written in Python
Command-line, PubChem PUG client, written in Python; developed for Linux -
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Pyntrez
Command-line, Entrez, NCBI e-utilities client, written in Python
Command-line, Entrez, NCBI e-utilities client, written in Python; developed for Linux -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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Pugsly PubChem Client
Command-line, PubChem PUG client, written in Python
Client to the PubChem Tool (PCT), The Power User Gateway (PUG). Written in Python and developed for use with Linux. -
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Pyntrez NCBI Database Client
Command-line, Entrez, NCBI e-utilities client, written in Python
Comman-line client to Entrez, e-utilities, written in Python, developed for Linux -
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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smalt
A mapper for DNA sequencing reads
SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming. -
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mPUMA
microbial Profiling Using Metagenomic Assembly
mPUMA: microbial Profiling Using Metagenomic Assembly This is a software package which was designed to allow researchers to profile microbial communities using a de novo assembly approach to form Operational Taxonomic Units (OTUs). While originally designed to support the analysis of cpn60 based amplicons, mPUMA can be used to analyze data from any suitable DNA barcode. A manuscript describing mPUMA is currently being developed and will be submitted for peer review presently. If... -
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Pathomx
Workflow-based data analysis built on IPython
Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. -
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IMPACT_S
Integrated Multiprogram Platform Analyze & Combine Tests of Selection
Maldonado E, Sunagar K, Almeida D, Vasconcelos V, Antunes A (2014) IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection. PLoS ONE 9(10): e96243. doi: https://doi.org/10.1371/journal.pone.0096243 -
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data... -
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nail_systems_biology
NAIL is a toolset for network analysis in the life sciences
The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results. These methods are designed as self-contained platform-independent components which can be called either from another program, or from a command line. Modelling biological systems as networks (graphs) is becoming a... -
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iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class. See the change log for full details.
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows... -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the... -
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CUSHAW2: Parallel Gapped Read Alignment
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. -
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FLASH
Merge mates from fragments that are shorter than twice the read length
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies. -
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Create, check, annotate, merge, diff, split SBML (System Biology Markup Lanugage) documents. The latest version of semanticSBML is webbased with a RESTful interface.
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
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Matchup
Bioinformatics tool for universal primers and group-specific probes
Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.