Showing 29 of total 29 results (show query)
bioc
DESeq2:Differential gene expression analysis based on the negative binomial distribution
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Maintained by Michael Love. Last updated 25 days ago.
sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp
375 stars 16.11 score 17k scripts 115 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructurebioconductor-packagecore-package
12 stars 14.22 score 612 scripts 2.2k dependents
metrumresearchgroup
mrgsolve:Simulate from ODE-Based Models
Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Maintained by Kyle T Baron. Last updated 11 days ago.
138 stars 10.90 score 1.2k scripts 3 dependentsbioc
ORFik:Open Reading Frames in Genomics
R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.
Maintained by Haakon Tjeldnes. Last updated 1 months ago.
immunooncologysoftwaresequencingriboseqrnaseqfunctionalgenomicscoveragealignmentdataimportcpp
33 stars 10.56 score 115 scripts 2 dependents
bioc
lemur:Latent Embedding Multivariate Regression
Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.
Maintained by Constantin Ahlmann-Eltze. Last updated 5 months ago.
transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionopenblascpp
87 stars 7.69 score 81 scripts
emitanaka
edibble:Encapsulating Elements of Experimental Design
A system to facilitate designing comparative (and non-comparative) experiments using the grammar of experimental designs <https://emitanaka.org/edibble-book/>. An experimental design is treated as an intermediate, mutable object that is built progressively by fundamental experimental components like units, treatments, and their relation. The system aids in experimental planning, management and workflow.
Maintained by Emi Tanaka. Last updated 5 hours ago.
216 stars 7.52 score 62 scriptsbioc
proDA:Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.
Maintained by Constantin Ahlmann-Eltze. Last updated 5 months ago.
proteomicsmassspectrometrydifferentialexpressionbayesianregressionsoftwarenormalizationqualitycontrol
19 stars 7.52 score 48 scripts 1 dependents
kkholst
targeted:Targeted Inference
Various methods for targeted and semiparametric inference including augmented inverse probability weighted (AIPW) estimators for missing data and causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>), variable importance and conditional average treatment effects (CATE) (van der Laan (2006) <doi:10.2202/1557-4679.1008>), estimators for risk differences and relative risks (Richardson et al. (2017) <doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).
Maintained by Klaus K. Holst. Last updated 2 months ago.
causal-inferencedouble-robustestimationsemiparametric-estimationstatisticsopenblascppopenmp
11 stars 7.20 score 30 scripts 1 dependentsbioc
GeomxTools:NanoString GeoMx Tools
Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial
7.11 score 239 scripts 3 dependentsbioc
isomiRs:Analyze isomiRs and miRNAs from small RNA-seq
Characterization of miRNAs and isomiRs, clustering and differential expression.
Maintained by Lorena Pantano. Last updated 5 months ago.
mirnarnaseqdifferentialexpressionclusteringimmunooncologyanalyze-isomirsbioconductorisomirs
8 stars 6.97 score 43 scriptsbioc
DRIMSeq:Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
Maintained by Malgorzata Nowicka. Last updated 5 months ago.
immunooncologysnpalternativesplicingdifferentialsplicinggeneticsrnaseqsequencingworkflowstepmultiplecomparisongeneexpressiondifferentialexpression
6.91 score 136 scripts 2 dependents
jazznbass
scan:Single-Case Data Analyses for Single and Multiple Baseline Designs
A collection of procedures for analysing, visualising, and managing single-case data. These include piecewise linear regression models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u', 'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions support outlier detection, handling missing values, scaling, and custom transformations. An export function helps to generate html, word, and latex tables in a publication friendly style. More details can be found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Maintained by Juergen Wilbert. Last updated 12 days ago.
4 stars 6.47 score 62 scripts 1 dependents
mdrcny
PUMP:Power Under Multiplicity Project
Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Maintained by Luke Miratrix. Last updated 1 months ago.
8 stars 6.45 score 13 scripts
victor-navarro
calmr:Canonical Associative Learning Models and their Representations
Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.
Maintained by Victor Navarro. Last updated 10 months ago.
3 stars 6.40 score 17 scriptsbioc
NanoStringNCTools:NanoString nCounter Tools
Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq
6.35 score 94 scripts 4 dependents
mingdeyu
dgpsi:Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations
Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process, and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package, see <https://mingdeyu.github.io/dgpsi-R/>.
Maintained by Deyu Ming. Last updated 6 days ago.
deep-gaussian-processesemulationgaussian-processessurrogate-models
6.03 score 76 scriptsbioc
TCseq:Time course sequencing data analysis
Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.
Maintained by Mengjun Wu. Last updated 5 months ago.
epigeneticstimecoursesequencingchipseqrnaseqdifferentialexpressionclusteringvisualization
5.92 score 28 scripts 1 dependents
llrs
experDesign:Design Experiments for Batches
Distributes samples in batches while making batches homogeneous according to their description. Allows for an arbitrary number of variables, both numeric and categorical. For quality control it provides functions to subset a representative sample.
Maintained by Lluís Revilla Sancho. Last updated 3 months ago.
10 stars 5.48 score 1 scripts
biometryhub
biometryassist:Functions to Assist Design and Analysis of Agronomic Experiments
Provides functions to aid in the design and analysis of agronomic and agricultural experiments through easy access to documentation and helper functions, especially for users who are learning these concepts. While not required for most functionality, this package enhances the `asreml` package which provides a computationally efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It is a commercial package that can be purchased as 'asreml-R' from 'VSNi' <https://vsni.co.uk/>, who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>).
Maintained by Sam Rogers. Last updated 10 months ago.
biometryexperimental-designteaching
8 stars 5.20 score 8 scripts
j-moravec
baffle:Make Waffle Plots with Base Graphics
Waffle plots are rectangular pie charts that represent a quantity or abundances using colored squares or other symbol. This makes them better at transmitting information as the discrete number of squares is easier to read than the circular area of pie charts. While the original waffle charts were rectangular with 10 rows and columns, with a single square representing 1%, they are nowadays popular in various infographics to visualize any proportional ratios.
Maintained by Jiří Moravec. Last updated 2 years ago.
5 stars 4.40 score 3 scriptsbioc
lmdme:Linear Model decomposition for Designed Multivariate Experiments
linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.
Maintained by Cristobal Fresno. Last updated 5 months ago.
microarrayonechanneltwochannelvisualizationdifferentialexpressionexperimentdatacancer
3.78 score 1 scripts
rbarfield
CpGassoc:Association Between Methylation and a Phenotype of Interest
Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Maintained by R Barfield. Last updated 9 months ago.
3.70 score 50 scripts
philippallmann
modest:Model-Based Dose-Escalation Trials
User-friendly Shiny apps for designing and evaluating phase I cancer clinical trials, with the aim to estimate the maximum tolerated dose (MTD) of a novel drug, using a Bayesian decision procedure based on logistic regression.
Maintained by Philip Pallmann. Last updated 7 years ago.
1 stars 3.30 score 9 scripts
arappold
docopulae:Optimal Designs for Copula Models
A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Maintained by Andreas Rappold. Last updated 6 years ago.
3.18 score 30 scripts
doer0
ibd:Incomplete Block Designs
A collection of several utility functions related to binary incomplete block designs. Contains function to generate A- and D-efficient binary incomplete block designs with given numbers of treatments, number of blocks and block size. Contains function to generate an incomplete block design with specified concurrence matrix. There are functions to generate balanced treatment incomplete block designs and incomplete block designs for test versus control treatments comparisons with specified concurrence matrix. Allows performing analysis of variance of data and computing estimated marginal means of factors from experiments using a connected incomplete block design. Tests of hypothesis of treatment contrasts in incomplete block design set up is supported.
Maintained by B N Mandal. Last updated 1 years ago.
2.95 score 33 scripts 3 dependents
shuaih0303
OWEA:Optimal Weight Exchange Algorithm for Optimal Designs for Three Models
An implementation of optimal weight exchange algorithm Yang(2013) <doi:10.1080/01621459.2013.806268> for three models. They are Crossover model with subject dropout, crossover model with proportional first order residual effects and interference model. You can use it to find either A-opt or D-opt approximate designs. Exact designs can be automatically rounded from approximate designs and relative efficiency is provided as well.
Maintained by Shuai Hao. Last updated 3 years ago.
2.70 score 4 scripts