Search Results for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files" - Page 7
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Showing 1243 open source projects for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files"
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Run applications fast and securely in a fully managed environmentRun frontend and backend services, batch jobs, deploy websites and applications, and queue processing workloads without the need to manage infrastructure.
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The AI workplace management platformBy combining AI workflows, predictive intelligence, and automated insights, OfficeSpace gives leaders a complete view of how their spaces are used and how people work. Facilities, IT, HR, and Real Estate teams use OfficeSpace to optimize space utilization, enhance employee experience, and reduce portfolio costs with precision.
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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PPIXpress
specific protein interaction networks from transcript expression
...Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 . -
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Peak List 2 MSP
Simple peak list to MSP file converter
Peak List 2 MSP takes your ascii mass/intensity pair list (or lists) and swaps them into MSP format (NIST standard text files for searching). It: takes lists from the clipboard (or drag and drop), sorts them by mass, normalises intensities, rejects below a cut off (that you define), adds MSP headers, puts the result back in the clipboard (or a file), has a command line interface so you can pass files in programmatically, has an api so you can call it in your own code (should you feel the urge). ... -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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The AI-powered unified PSA-RMM platform for modern MSPs.SuperOps.ai is the only PSA-RMM platform powered by intelligent automation and thoughtfully crafted for the new-age MSP. The platform also helps MSPs manage their projects, clients, and IT documents from a single place.
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...A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007/s13127-011-0056-0
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PANDA-view
An easy-to-use tool for data visualization and statistical analysis
PANDA-view, an affiliated tool of PANDA, includes the methods for differentially expressed protein detection, missing value imputation and the parametric and non-parametric statistical tests. Meanwhile, the most commonly-used data visualization methods are also implemented in PANDA-view. -
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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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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer... -
Securden Privileged Account ManagerDiscover and manage administrator, service, and web app passwords, keys, and identities. Automate management with approval workflows. Centrally control, audit, monitor, and record all access to critical IT assets.
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. ... -
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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. Use this software freely and fight the Remote Neural Monitoring system. -
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MGF2MGF CH
Convert mgf mass values to their nearest elemental formula
MGF2MGF CH processes mgf files (mascot generic format). It: converts masses to their nearest elemental formula mass (provided that you supply an empirical formula), can normalise intensities to the base peak of a block of ions, produces a new file with the prefix of your choice. You: specify the input line that contains the empirical formula of the parent ion, specify the key that identifies a formula and then the formula) separated by one space character, either drag and drop mgf files onto the window, or pass filenames though a command line argument. ... -
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reditools
RNA editing detection by NGS data
REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data. RNA editing is a post-transcriptional phenomenon involving the insertion/deletion or substitution of specific bases in precise RNA localizations. In human, RNA editing occurs by deamination of cytosine to uridine (C-to-U) or mostly by the adenosine to inosine (A-to-I) conversion through ADAR enzymes. A-to-I substitutions may have profound functional consequences and have been linked to a variety of human diseases including neurological and neurodegenerative disorders or cancer. ... -
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CompleXChange
differential analysis of combinatorial protein complexes
The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
...It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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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.
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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...The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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A key goal for NEMO is the development of a formal logic (“ontology”) to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, different experiment paradigms, and different modalities (EEG/MEG)
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing. -
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HSRA
Hadoop spliced read aligner for RNA-seq data
...This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The profile is obtained by calculating the genome-wide Pearson correlation coefficient (R) between the genomic variable values and the TSS (or TTS) counts at incremental shifting of transcribed strand. The data of TSS and TTS counts used to compute the profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting R values for the various shifts of variable coordinates with respect to TSS or TTS. ... -
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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rMATS-ISO
rMATS-Iso is a generalization of rMATS for complex splicing patterns.
rMATS-Iso is a generalization of the rMATS statistical framework, to detect differential splicing modules with complex splicing patterns using replicate RNA-seq data. -
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GMOL
A tool for 3D genome structure visualization
...It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. ...
