Showing 50 of total 50 results (show query)
eddelbuettel
digest:Create Compact Hash Digests of R Objects
Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Maintained by Dirk Eddelbuettel. Last updated 2 months ago.
79.9 match 114 stars 19.82 score 11k scripts 6.9k dependents
hrbrmstr
tdigest:Wicked Fast, Accurate Quantiles Using t-Digests
The t-Digest construction algorithm, by Dunning et al., (2019) <doi:10.48550/arXiv.1902.04023>, uses a variant of 1-dimensional k-means clustering to produce a very compact data structure that allows accurate estimation of quantiles. This t-Digest data structure can be used to estimate quantiles, compute other rank statistics or even to estimate related measures like trimmed means. The advantage of the t-Digest over previous digests for this purpose is that the t-Digest handles data with full floating point resolution. The accuracy of quantile estimates produced by t-Digests can be orders of magnitude more accurate than those produced by previous digest algorithms. Methods are provided to create and update t-Digests and retrieve quantiles from the accumulated distributions.
Maintained by Bob Rudis. Last updated 9 months ago.
21.0 match 37 stars 5.35 score 10 scripts 4 dependents
bioc
cleaver:Cleavage of Polypeptide Sequences
In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html
Maintained by Sebastian Gibb. Last updated 5 months ago.
proteomicsbioccleavagedigestpeptides
12.2 match 12 stars 7.46 score 22 scripts 2 dependents
rte-antares-rpackage
antaresRead:Import, Manipulate and Explore the Results of an 'Antares' Simulation
Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://antares-simulator.org/>).
Maintained by Tatiana Vargas. Last updated 3 days ago.
infrastructuredataimportadequacybilanelectricityenergyhdf5linear-algebramonte-carlo-simulationoptimisationprevisionnelrhdf5rtesimulationtyndp
6.0 match 13 stars 9.45 score 148 scripts 3 dependentsbioc
gdsfmt:R Interface to CoreArray Genomic Data Structure (GDS) Files
Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.
Maintained by Xiuwen Zheng. Last updated 2 days ago.
infrastructuredataimportbioinformaticsgds-formatgenomicscpp
4.1 match 18 stars 11.34 score 920 scripts 29 dependents
dipterix
dipsaus:A Dipping Sauce for Data Analysis and Visualizations
Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Maintained by Zhengjia Wang. Last updated 5 days ago.
5.1 match 13 stars 7.90 score 85 scripts 3 dependents
s-u
PKI:Public Key Infrastucture for R Based on the X.509 Standard
Public Key Infrastucture functions such as verifying certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.
Maintained by Simon Urbanek. Last updated 7 months ago.
3.9 match 18 stars 8.52 score 63 scripts 8 dependentsbioc
tximeta:Transcript Quantification Import with Automatic Metadata
Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.
Maintained by Michael Love. Last updated 2 months ago.
annotationgenomeannotationdataimportpreprocessingrnaseqsinglecelltranscriptomicstranscriptiongeneexpressionfunctionalgenomicsreproducibleresearchreportwritingimmunooncology
2.8 match 67 stars 10.58 score 466 scripts 1 dependents
ropensci
redland:RDF Library Bindings in R
Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Maintained by Matthew B. Jones. Last updated 1 years ago.
3.8 match 17 stars 7.85 score 98 scripts 13 dependentsbioc
glmSparseNet:Network Centrality Metrics for Elastic-Net Regularized Models
glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".
Maintained by André Veríssimo. Last updated 5 months ago.
softwarestatisticalmethoddimensionreductionregressionclassificationsurvivalnetworkgraphandnetwork
3.8 match 6 stars 7.42 score 41 scripts 1 dependents
jeroen
openssl:Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Maintained by Jeroen Ooms. Last updated 1 months ago.
1.5 match 65 stars 18.00 score 632 scripts 5.0k dependents
predictiveecology
reproducible:Enhance Reproducibility of R Code
A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().
Maintained by Eliot J B McIntire. Last updated 1 months ago.
reproducibilityreproducible-research
2.3 match 41 stars 10.52 score 122 scripts 15 dependentsbioc
SeqArray:Data Management of Large-Scale Whole-Genome Sequence Variant Calls
Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.
Maintained by Xiuwen Zheng. Last updated 10 days ago.
infrastructuredatarepresentationsequencinggeneticsbioinformaticsgds-formatsnpsnvweswgscpp
2.0 match 45 stars 12.08 score 1.1k scripts 9 dependentsbioc
PLSDAbatch:PLSDA-batch
A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.
Maintained by Yiwen (Eva) Wang. Last updated 5 months ago.
statisticalmethoddimensionreductionprincipalcomponentclassificationmicrobiomebatcheffectnormalizationvisualization
4.0 match 13 stars 5.37 score 18 scriptsbioc
REDseq:Analysis of high-throughput sequencing data processed by restriction enzyme digestion
The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
Maintained by Lihua Julie Zhu. Last updated 5 months ago.
sequencingsequencematchingpreprocessing
6.2 match 3.48 score 15 scriptspredictiveecology
SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models
Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).
Maintained by Eliot J B McIntire. Last updated 19 days ago.
discrete-events-simulationssimulation-frameworksimulation-modeling
1.9 match 10 stars 10.61 score 142 scripts 6 dependents
cran
OrgMassSpecR:Organic Mass Spectrometry
Organic/biological mass spectrometry data analysis.
Maintained by Nathan Dodder. Last updated 8 years ago.
5.1 match 3.68 score 2 dependentsbioc
UMI4Cats:UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.
Maintained by Mireia Ramos-Rodriguez. Last updated 5 months ago.
qualitycontrolpreprocessingalignmentnormalizationvisualizationsequencingcoveragechromatinchromatin-interactiongenomicsumi4c
3.3 match 5 stars 5.57 score 7 scripts
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
1.8 match 67 stars 9.94 score 436 scripts 2 dependents
statmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
3.6 match 5 stars 4.94 score 544 scriptsbioc
DECIPHER:Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences.
Maintained by Erik Wright. Last updated 5 days ago.
clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionopenmp
1.9 match 8.40 score 1.1k scripts 14 dependentsdipterix
threeBrain:Your Advanced 3D Brain Visualization
A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://rave.wiki>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check citation("threeBrain") for details.
Maintained by Zhengjia Wang. Last updated 2 days ago.
brainecogelectroencephalographyieeglocalizationmri-brainneuroimagingtemplate-brains
1.9 match 44 stars 8.24 score 38 scripts 1 dependentsbioc
Basic4Cseq:Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
Maintained by Carolin Walter. Last updated 5 months ago.
immunooncologyvisualizationqualitycontrolsequencingcoveragealignmentrnaseqsequencematchingdataimport
3.9 match 3.30 score 5 scripts
bioc
deepSNV:Detection of subclonal SNVs in deep sequencing data.
This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.
Maintained by Moritz Gerstung. Last updated 5 months ago.
geneticvariabilitysnpsequencinggeneticsdataimportcurlbzip2xz-utilszlibcpp
1.6 match 6.53 score 38 scripts 1 dependents
jhudsl
crsra:Tidying and Analyzing 'Coursera' Research Export Data
Tidies and performs preliminary analysis of 'Coursera' research export data. These export data can be downloaded by anyone who has classes on Coursera and wants to analyze the data. Coursera is one of the leading providers of MOOCs and was launched in January 2012. With over 25 million learners, Coursera is the most popular provider in the world being followed by EdX, the MOOC provider that was a result of a collaboration between Harvard University and MIT, with over 10 million users. Coursera has over 150 university partners from 29 countries and offers a total of 2000+ courses from computer science to philosophy. Besides, Coursera offers 180+ specialization, Coursera's credential system, and four fully online Masters degrees. For more information about Coursera check Coursera's About page on <https://blog.coursera.org/about/>.
Maintained by Aboozar Hadavand. Last updated 4 years ago.
2.5 match 2 stars 4.15 score 14 scripts
ttspackage
trustedtimestamping:Create Trusted Timestamps of Datasets and Files
Trusted Timestamps (tts) are created by incorporating a hash of a file or dataset into a transaction on the decentralized blockchain (Stellar network). The package makes use of a free service provided by <https://stellarapi.io>.
Maintained by Peter Muller. Last updated 6 years ago.
3.3 match 3 stars 3.18 score
syedhaider5
chicane:Capture Hi-C Analysis Engine
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Maintained by Syed Haider. Last updated 3 years ago.
3.8 match 2.75 score 28 scripts
learnitr
learnitgrid:Manage Rubrics or Assessment Grids for GitHub Repositories
Create and manage semi-automatically rubrics to assess GitHub projects (R scripts, R Markdown or Quarto files). Create directed projects where students have to complete documents and submit them to GitHub (classroom) so that they are evaluated using the rubric (or assessment grid).
Maintained by Philippe Grosjean. Last updated 9 months ago.
3.3 match 1 stars 3.00 score 7 scriptsbioc
MassArray:Analytical Tools for MassArray Data
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.
Maintained by Reid F. Thompson. Last updated 5 months ago.
immunooncologydnamethylationsnpmassspectrometrygeneticsdataimportvisualization
2.3 match 4.30 score 1 scripts
reedacartwright
rbedrock:Analysis and Manipulation of Data from Minecraft Bedrock Edition
Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
Maintained by Reed Cartwright. Last updated 18 days ago.
1.8 match 43 stars 5.24 score 3 scripts
benbruyneel
massSpectrometryR:massSpectrometryR
Provides calculations, plotting etc for chemistry & mass spectrometry.
Maintained by Ben Bruyneel. Last updated 4 months ago.
mass-spectrometryproteomicsopenjdk
5.3 match 1.70 score 1 scripts
ekstroem
isdals:Datasets for Introduction to Statistical Data Analysis for the Life Sciences
Provides datasets for the book "Introduction to Statistical Data Analysis for the Life Sciences, Second edition" by Ekstrøm and Sørensen (2014).
Maintained by Claus Ekstrom. Last updated 2 years ago.
3.4 match 2.51 score 108 scripts 1 dependentseddelbuettel
RcppFarmHash:Interface to the Google 'FarmHash' Family of Hash Functions
The Google 'FarmHash' family of hash functions is used by the Google 'BigQuery' data warehouse via the 'FARM_FINGERPRINT' function. This package permits to calculate these hash digest fingerprints directly from R, and uses the included 'FarmHash' files written by G. Pike and copyrighted by Google, Inc.
Maintained by Dirk Eddelbuettel. Last updated 6 months ago.
2.3 match 2 stars 3.48 score 2 scriptsbioc
adductomicsR:Processing of adductomic mass spectral datasets
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
Maintained by Josie Hayes. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui
1.8 match 1 stars 4.00 score 5 scripts
s-fleck
lgrExtra:Extra Appenders for 'lgr'
Additional appenders for the logging package 'lgr' that support logging to databases, email and push notifications.
Maintained by Stefan Fleck. Last updated 7 months ago.
1.7 match 7 stars 3.54 score 3 scriptsbenbruyneel
proteinDiscover:ProteinDiscover
Provides an interface to the data contained in Proteome Discoverer (Thermo Scientific) results.
Maintained by Ben Bruyneel. Last updated 1 years ago.
mass-spectrometryproteomicsproteomics-data-analysis
1.6 match 2 stars 3.00 score 2 scriptscran
bspmma:Bayesian Semiparametric Models for Meta-Analysis
The main functions carry out Gibbs' sampler routines for nonparametric and semiparametric Bayesian models for random effects meta-analysis.
Maintained by Deborah Burr. Last updated 6 years ago.
3.5 match 1.00 score
jbgruber
rwhatsapp:Import and Handling for 'WhatsApp' Chat Logs
A straightforward, easy-to-use and robust parsing package which aims to digest history files from the popular messenger service 'WhatsApp' in all locales and from all devices.
Maintained by Johannes Gruber. Last updated 1 years ago.
0.5 match 97 stars 6.24 score 36 scriptsbioc
VplotR:Set of tools to make V-plots and compute footprint profiles
The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.
Maintained by Jacques Serizay. Last updated 5 months ago.
nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment
0.5 match 10 stars 5.64 score 11 scripts
crowding
memo:In-Memory Caching of Repeated Computations (Memoization)
A simple in-memory, LRU cache that can be wrapped around any function to memoize it. The cache is keyed on a hash of the input data (using 'digest') or on pointer equivalence.
Maintained by Peter Meilstrup. Last updated 1 years ago.
0.5 match 13 stars 5.26 score 28 scripts
kuadrat
growR:Implementation of the Vegetation Model ModVege
Run grass growth simulations using a grass growth model based on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. Model Description." (2006) <doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in this package contains a few additions to the above cited version of ModVege, such as simulations of management decisions, and influences of snow cover. As such, the model is fit to simulate grass growth in mountainous regions, such as the Swiss Alps. The package also contains routines for calibrating the model and helpful tools for analysing model outputs and performance.
Maintained by Kevin Kramer. Last updated 7 months ago.
agronomygrassgrasslandmodellingsimulation-modeling
0.5 match 3 stars 5.28 score 14 scripts
cstewartgh
QFASA:Quantitative Fatty Acid Signature Analysis
Accurate estimates of the diets of predators are required in many areas of ecology, but for many species current methods are imprecise, limited to the last meal, and often biased. The diversity of fatty acids and their patterns in organisms, coupled with the narrow limitations on their biosynthesis, properties of digestion in monogastric animals, and the prevalence of large storage reservoirs of lipid in many predators, led to the development of quantitative fatty acid signature analysis (QFASA) to study predator diets.
Maintained by Connie Stewart. Last updated 7 months ago.
0.5 match 1 stars 4.83 score 17 scripts
zhuobie
smcryptoR:ShangMi(SM) Cryptographic Algorithms(SM2/SM3/SM4)
Bindings to 'smcrypto' <https://github.com/zhuobie/smcrypto>: a 'Rust' implementation of China's Standards of Encryption Algorithms, which is usually called 'ShangMi(SM)' algorithms. It contains 'SM3' message digest algorithm, 'SM2' asymmetric encryption algorithm and 'SM4' symmetric encryption algorithm. Users can do message hash, encrypt/decrypt, sign/verify, key exchange and more.
Maintained by Meng Yu. Last updated 12 months ago.
0.5 match 1 stars 4.30 score 1 scripts
sudoms
freqpcr:Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk Samples
Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
Maintained by Masaaki Sudo. Last updated 3 years ago.
bioinformaticsfrequency-estimationpcrstatistics
0.5 match 1 stars 3.70 score 4 scriptsbioc
deltaCaptureC:This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.
Maintained by Michael Shapiro. Last updated 5 months ago.
biologicalquestionstatisticalmethod
0.5 match 3.48 score 1 scripts
shashankkumbhare
ypssc:Yeast-Proteome Secondary-Structure Calculator
An extension for 'NetSurfP-2.0' (Klausen et al. (2019) <doi:10.1002/prot.25674>) which is specifically designed to analyze the results of bottom-up-proteomics that is primarily analyzed with 'MaxQuant' (Cox, J., Mann, M. (2008) <doi:10.1038/nbt.1511>). This tool is designed to process a large number of yeast peptides that produced as a results of whole yeast cell-proteome digestion and provide a coherent picture of secondary structure of proteins.
Maintained by Shashank Kumbhare. Last updated 3 years ago.
0.5 match 2.70 score 1 scripts
r-simmer
simmer.json:Translates JSON into a simmer environment
Define a simmer simulation problem using JSON syntax. This makes for easy sharing of simulation definitions and for easily digesting a simulation definition through an API.
Maintained by Bart Smeets. Last updated 9 years ago.
discrete-eventjsonserializationsimulation
0.5 match 4 stars 2.30 score 4 scripts
