Search Results for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files" - Page 2
Sort By:
Showing 166 open source projects for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files"
View related business solutions-
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.
-
Get full visibility and control over your tasks and projects with Wrike.Wrike offers world-class features that empower cross-functional, distributed, or growing teams take their projects from the initial request stage all the way to tracking work progress and reporting results.
-
1
Xtraq
Xtraq extracts iTRAQ data from .ANZ Peaks results files
Xtraq extracts iTRAQ data from .ANZ Peaks results files. -
2
Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this... -
3
CBMPy
PySCeS Constraint Based Modelling
...CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. CBMPy supports user interaction via: - interactive console or as a library for advanced use - GUI, visual representation of the model, analysis methods - a SOAP based webAPI exposes high level functionality via web services -
4
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 -
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.
-
5
TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and... -
6
LymPHOS2
LymPHOS2 Web-App
...Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012 -
7
HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremely challenging, particularly on a whole-genome scale. ... -
8
DEBay
Deconvolutes qPCR data to estimate cell-type-specific gene expression
...The user manual of DEBay: https://sourceforge.net/projects/debay/files/UserManual.pdf Sample data: https://sourceforge.net/projects/debay/files/Test_data/ Citation Information: Vimalathithan Devaraj, Biplab Bose. DEBay: A computational tool for deconvolution of quantitative PCR data for estimation of cell type-specific gene expression in a mixed population. Heliyon, 2020, 6(7), e04489. https://doi.org/10.1016/j.heliyon.2020.e04489 -
9
PBTK Optimizer
Application for optimization of parameters in PBTK models
...Other parameters can be determined through in-vitro experiments or through extrapolation using published equations. When it is impractical to use these methods to estimate a parameter, techniques can be used to optimize parameters so that model results best fit validation data. This tool was designed to optimize a user-specified list of parameters to a user-specified PBTK model. The user also controls validation data and optimization algorithms. In addition to optimized parameters, the tool outputs statistical information about the fit of the optimized model. -
Creatio Low-Code Development PlatformIntelligent low-code platform to empower both IT and non-IT staff to effortlessly build enterprise-grade apps and processes
-
10
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).
-
11
...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
-
12
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. ... -
13
PyTom
http://www.sciencedirect.com/science/article/pii/S1047847711003492
PyTom is a toolbox developed for interpreting cryo electron tomography data. All steps from reconstruction, localization, alignment and classification are covered with standard and improved methods. Please sign up to our mailing list to keep up with the most recent updates and versions. -
14
YFitter
Fitting Y chromosome haplogroups by maximum likelihood
Yfitter is a program for assigning Y chromosome haplogroups to individuals sequenced at low coverage. It is designed to be used in a samtools/bcftools pipeline. Yfitter also supports haplogrouping using chip genotype data. -
15
PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
16
lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
17
DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
This project contains Python scripts usable for a dual transcript-discovery approach that improves the delimitation of gene features from RNA-seq data in the chicken model. Documentation: http://bio.biologists.org/content/biolopen/suppl/2018/01/17/bio.028498.DC1/BIO028498supp.pdf Citation: Orgeur M., Martens M., Börno S. T., Timmermann B., Duprez D. and Stricker S. (2018). A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. ... -
18
Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
-
19
MethyMer
Design of specific primer combinations for bisulfite sequencing
...SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation (microarrays) and gene expression (RNA-Seq) data, as well as methylation-expression correlation analysis results for 20 human cancer types. ENCODE genome regions annotation data are also integrated in MethyMer -
20
Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. The 28 partners of CCPN jointly cover all aspects of biomolecular NMR and together they promote excellence in science in their respective fields. -
21
...New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
-
22
nmr-nessy
NMR relaxation dispersion spectroscopy analysis software
NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. -
23
SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. -
24
CorNetMap
A tool for Gene Expression Correlation Network
...How to use and doccumentation: https://sourceforge.net/projects/cornetmap/files/Documentation_corNetMap.pdf Sample data for testing: https://sourceforge.net/projects/cornetmap/files/Test%20Data/ Citation: Cite CornetMap as " Khaund, A. Bose, B. CorNetMap. https://sourceforge.net/projects/cornetmap " Credit: Abhigyan Khaund, Biplab Bose, IIT Guwahati -
25
PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to...
