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tianshu129

foqat:Field Observation Quick Analysis Toolkit

Tools for quickly processing and analyzing field observation data and air quality data. This tools contain functions that facilitate analysis in atmospheric chemistry (especially in ozone pollution). Some functions of time series are also applicable to other fields. For detail please view homepage<https://github.com/tianshu129/foqat>. Scientific Reference: 1. The Hydroxyl Radical (OH) Reactivity: Roger Atkinson and Janet Arey (2003) <doi:10.1021/cr0206420>. 2. Ozone Formation Potential (OFP): <https://ww2.arb.ca.gov/sites/default/files/classic/regact/2009/mir2009/mir10.pdf>, Zhang et al.(2021) <doi:10.5194/acp-21-11053-2021>. 3. Aerosol Formation Potential (AFP): Wenjing Wu et al. (2016) <doi:10.1016/j.jes.2016.03.025>. 4. TUV model: <https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model>.

Maintained by Tianshu Chen. Last updated 6 months ago.

air-pollutionair-qualityair-quality-dataair-quality-measurementsair-quality-monitorair-quality-reportsair-quality-sensoratmospheric-chemistryatmospheric-modellingatmospheric-sciencedaily-maximum-8-hour-ozonefield-observationmirofpozone-formation-potentialphotolysis-rate-coefficientstime-seriestime-series-analysistuv

11.0 match 35 stars 4.54 score 20 scripts

meer-1

PRNG:A Pseudo-Random Number Generator

Provides functions for generating pseudo-random numbers that follow a uniform distribution [0,1]. Randomness tests were conducted using the National Institute of Standards and Technology test suite<https://csrc.nist.gov/pubs/sp/800/22/r1/upd1/final>, along with additional tests. The sequence generated depends on the initial values and parameters. The package includes a linear congruence map as the decision map and three chaotic maps to generate the pseudo-random sequence, which follow a uniform distribution. Other distributions can be generated from the uniform distribution using the Inversion Principle Method and BOX-Muller transformation. Small perturbations in seed values result in entirely different sequences of numbers due to the sensitive nature of the maps being used. The chaotic nature of the maps helps achieve randomness in the generator. Additionally, the generator is capable of producing random bits.

Maintained by Sajad Ahmad Mir. Last updated 6 months ago.

8.2 match 3.18 score 5 scripts

yufree

enviGCMS:GC/LC-MS Data Analysis for Environmental Science

Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.

Maintained by Miao YU. Last updated 2 months ago.

environmentmass-spectrometrymetabolomics

3.8 match 17 stars 6.49 score 30 scripts 1 dependents

bioc

circRNAprofiler:circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

Maintained by Simona Aufiero. Last updated 5 months ago.

annotationstructuralpredictionfunctionalpredictiongenepredictiongenomeassemblydifferentialexpression

3.8 match 10 stars 5.78 score 5 scripts

aphalo

photobiologyWavebands:Waveband Definitions for UV, VIS, and IR Radiation

Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 8 months ago.

3.3 match 1 stars 6.53 score 378 scripts 3 dependents

bioc

scanMiR:scanMiR

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

mirnasequencematchingalignment

3.5 match 5.89 score 52 scripts 1 dependents

bioc

ExiMiR:R functions for the normalization of Exiqon miRNA array data

This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.

Maintained by Sylvain Gubian. Last updated 5 months ago.

microarrayonechanneltwochannelpreprocessinggeneexpressiontranscription

6.5 match 2.78 score 3 scripts

bioc

padma:Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.

Maintained by Andrea Rau. Last updated 5 months ago.

softwarestatisticalmethodprincipalcomponentgeneexpressionpathwaysrnaseqbiocartamethylseq

3.5 match 3 stars 4.95 score 2 scripts

miguelro

Relectoral:Electoral Analysis

Functions to obtain an important number of electoral indicators described in the package, which can be divided into two large sections: The first would be the one containing the indicators of electoral disproportionality, such as, Rae index, Loosemore–Hanby index, etc. The second group is intended to study the dimensions of the party system vote, through the indicators of electoral fragmentation, polarization, volatility, etc. Moreover, multiple seat allocation simulations can also be performed based on different allocation systems, such as the D'Hondt method, Sainte-Laguë, etc. Finally, some of these functions have been built so that, if the user wishes, the data provided by the Spanish Ministry of Home Office for different electoral processes held in Spain can be obtained automatically. All the above will allow the users to carry out deep studies on the results obtained in any type of electoral process. The methods are described in: Oñate, Pablo and Ocaña, Francisco A. (1999, ISBN:9788474762815); Ruiz Rodríguez, Leticia M. and Otero Felipe, Patricia (2011, ISBN:9788474766226).

Maintained by Miguel Rodríguez Asensio. Last updated 5 years ago.

openjdk

4.9 match 2.00 score

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Maintained by Martin R. Smith. Last updated 1 months ago.

evolutionary-biologyphylogenetic-treesphylogeneticscpp

0.5 match 21 stars 9.92 score 124 scripts 10 dependents

bioc

IntramiRExploreR:Predicting Targets for Drosophila Intragenic miRNAs

Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.

Maintained by Surajit Bhattacharya. Last updated 5 months ago.

softwaremicroarraygenetargetstatisticalmethodgeneexpressiongeneprediction

1.0 match 4.60 score 4 scripts

stephanartmann

miRtest:Combined miRNA- And mRNA-Testing

Package for combined miRNA- and mRNA-testing.

Maintained by Stephan Artmann. Last updated 1 years ago.

2.3 match 1 stars 2.08 score 12 scripts

bioc

multiMiR:Integration of multiple microRNA-target databases with their disease and drug associations

A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).

Maintained by Spencer Mahaffey. Last updated 5 months ago.

mirnadatahomo_sapiens_datamus_musculus_datarattus_norvegicus_dataorganismdatamicrorna-sequencesql

0.5 match 20 stars 8.45 score 141 scripts

abeith

retimer:Retime and Analyse Speech Signals

Retime speech signals with a native Waveform Similarity Overlap-Add (WSOLA) implementation translated from the 'TSM toolbox' by Driedger & Müller (2014) <https://www.audiolabs-erlangen.de/content/resources/MIR/TSMtoolbox/2014_DriedgerMueller_TSM-Toolbox_DAFX.pdf>. Design retimings and pitch (f0) transformations with tidy data and apply them via 'Praat' interface. Produce spectrograms, spectra, and amplitude envelopes. Includes implementation of vocalic speech envelope analysis (fft_spectrum) technique and example data (mm1) from Tilsen, S., & Johnson, K. (2008) <doi:10.1121/1.2947626>.

Maintained by Alistair Beith. Last updated 3 months ago.

0.5 match 4.18 score 5 scripts

cran

DNAmotif:DNA Sequence Motifs

Motifs within biological sequences show a significant role. This package utilizes a user-defined threshold value (window size and similarity) to create consensus segments or motifs through local alignment of dynamic programming with gap and it calculates the frequency of each identified motif, offering a detailed view of their prevalence within the dataset. It allows for thorough exploration and understanding of sequence patterns and their biological importance.

Maintained by Subham Ghosh. Last updated 6 months ago.

cpp

1.6 match 1.30 score

bmgfiasri

HEssRNA:Heritability-Based Estimation of Sample Size for RNA-Seq Data

Provides tools for estimating sample sizes primarily based on heritability, while also considering additional parameters such as statistical power and fold change. The package normalizes heritability values according to trait-specific heritability and classification to enhance accuracy in sample size estimation.

Maintained by Sarika Jaiswal. Last updated 2 months ago.

1.6 match 1.00 score

imiqbal

ImCluster:Efficiency of Cluster Sampling for Crop Surveys

Cluster sampling is a valuable approach when constructing a comprehensive list of individual units is challenging. It provides operational and cost advantages. This package is designed to test the efficiency of cluster sampling in terms cluster variance and design effect in context to crop surveys. This package has been developed using the algorithm of Iqbal et al. (2018) <doi:10.19080/BBOAJ.2018.05.555673>.

Maintained by M. Iqbal Jeelani. Last updated 1 years ago.

1.6 match 1.00 score

cran

SoilFDA:Fractal Dimension Analysis of Soil Particle Size Distribution

Function for the computation of fractal dimension based on mass of soil particle size distribution by Tyler & Wheatcraft (1992) <doi:10.2136/sssaj1992.03615995005600020005x>. It also provides functions for calculation of mean weight and geometric mean diameter of particle size distribution by Perfect et al. (1992) <doi:10.2136/sssaj1992.03615995005600050012x>.

Maintained by Fehim Jeelani Wani. Last updated 10 months ago.

1.5 match 1.00 score

imiqbal

ImFoR:Non-Linear Height Diameter Models for Forestry

Tree height is an important dendrometric variable and forms the basis of vertical structure of a forest stand. This package will help to fit and validate various non-linear height diameter models for assessing the underlying relationship that exists between tree height and diameter at breast height in case of conifer trees. This package has been implemented on Naslund, Curtis, Michailoff, Meyer, Power, Michaelis-Menten and Wykoff non linear models using algorithm of Huang et al. (1992) <doi:10.1139/x92-172> and Zeide et al. (1993) <doi:10.1093/forestscience/39.3.594>.

Maintained by M. Iqbal Jeelani. Last updated 1 years ago.

1.5 match 1.00 score

imiqbal

ImNN:Neural Networks for Predicting Volume of Forest Trees

Neural network has potential in forestry modelling. This package is designed to create and assess Artificial Intelligence based Neural Networks with varying architectures for prediction of volume of forest trees using two input features: height and diameter at breast height, as they are the key factors in predicting volume, therefore development and validation of efficient volume prediction neural network model is necessary. This package has been developed using the algorithm of Tabassum et al. (2022) <doi:10.18805/ag.D-5555>.

Maintained by M. Iqbal Jeelani. Last updated 1 years ago.

1.5 match 1.00 score

imiqbal

ImHD:Artificial Intelligence Based Machine Learning Algorithms for Height Diameter Relationships of Conifer Trees

Estimating height of forest plant is one of the key challenges of recent times. This package will help to fit and validate AI (Artificial Intelligence) based machine learning algorithms for estimation of height of conifer trees based on diameter at breast height as explanatory variable using algorithm of Paul et al. (2022) <doi:10.1371/journal.pone.0270553>..

Maintained by Dr. M. Iqbal Jeelani. Last updated 2 years ago.

1.5 match 1.00 score

ms609

TotalCopheneticIndex:Quantify the Balance of Phylogenetic Trees

Measures the degree of balance for a given phylogenetic tree by calculating the Total Cophenetic Index. Reference: A. Mir, F. Rossello, L. A. Rotger (2013). A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.

Maintained by Martin R. Smith. Last updated 4 years ago.

0.5 match 1.70 score 3 scripts

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