Light weight implementation of the standard distribution functions for the chi distribution, wrapping those for the chi-squared distribution in the stats package.

API Client for the Climate Hazards Center CHIRPS and CHIRTS'. The CHIRPS data is a quasi-global (50°S â 50°N) high-resolution (0.05 arc-degrees) rainfall data set, which incorporates satellite imagery and in-situ station data to create gridded rainfall time series for trend analysis and seasonal drought monitoring. CHIRTS is a quasi-global (60°S â 70°N), high-resolution data set of daily maximum and minimum temperatures. For more details on CHIRPS and CHIRTS data please visit its official home page <https://www.chc.ucsb.edu/data>.

The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>). chillR contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. chillR also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, chillR contains a function for interpolating hourly temperature records.

This package provides a pipeline for analysing Capture Hi-C data.

This package provides tools for processing short read data from ChIPseq experiments.

Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks.

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.

This package provides a collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets.

This package provides tools for connecting to CHILDES', an open repository for transcripts of parent-child interaction. For more information on the underlying data, see <https://langcog.github.io/childes-db-website/>.

Calculation of standard deviation scores and percentiles adduced from different standards (WHO, UK, Germany, Italy, China, etc). Also, references for laboratory values in children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. See package documentation for full list.

Reads demographic data from a variety of public data sources, extracting and harmonizing variables useful for the study of childfree individuals. The identification of childfree individuals and those with other family statuses uses Neal & Neal's (2024) "A Framework for Studying Adults who Neither have Nor Want Children" <doi:10.1177/10664807231198869>; A pre-print is available at <doi:10.31234/osf.io/fa89m>.

This package provides the facility to perform the chi-square and G-square test of independence, calculates the retrospective power of the traditional chi-square test, compute permutation and Monte Carlo p-value, and provides measures of association for tables of any size such as Phi, Phi corrected, odds ratio with 95 percent CI and p-value, Yule Q and Y, adjusted contingency coefficient, Cramer's V, V corrected, V standardised, bias-corrected V, W, Cohen's w, Goodman-Kruskal's lambda, and tau. It also calculates standardised, moment-corrected standardised, and adjusted standardised residuals, and their significance, as well as the Quetelet Index, IJ association factor, and adjusted standardised counts. It also computes the chi-square-maximising version of the input table. Different outputs are returned in nicely formatted tables.

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Mapas terrestres con topologias simplificadas. Estos mapas no tienen precision geodesica, por lo que aplica el DFL-83 de 1979 de la Republica de Chile y se consideran referenciales sin validez legal. No se incluyen los territorios antarticos y bajo ningun evento estos mapas significan que exista una cesion u ocupacion de territorios soberanos en contra del Derecho Internacional por parte de Chile. Esta paquete esta documentado intencionalmente en castellano asciificado para que funcione sin problema en diferentes plataformas. (Terrestrial maps with simplified toplogies. These maps lack geodesic precision, therefore DFL-83 1979 of the Republic of Chile applies and are considered to have no legal validity. Antartic territories are excluded and under no event these maps mean there is a cession or occupation of sovereign territories against International Laws from Chile. This package was intentionally documented in asciified spanish to make it work without problem on different platforms.).

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

Calculates the chilling and heat accumulation for studies of the temperate fruit trees. The models in this package are: Utah (Richardson et al., 1974, ISSN:0018-5345), Positive Chill Units - PCU (Linsley-Noaks et al., 1995, ISSN:1017-0316), GDH-A - Growing Degree Hours by Anderson et al.(1986, ISSN:0567-7572), GDH-R - Growing Degree Hours by Richardson et al.(1975, ISSN:0018-5345), North Carolina (Shaltout e Unrath, 1983, ISSN:0003-1062), Landsberg Model (Landsberg, 1974, ISSN:0305-7364), Q10 Model (Bidabe, 1967, ISSN:0031-9368), Jones Model (Jones et al., 2013 <DOI:10.1111/j.1438-8677.2012.00590.x>), Low-Chill Model (Gilreath and Buchanan, 1981, ISSN:0003-1062), Model for Cherry "Sweetheart" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Model for apple "Gala" (Guak and Nielsen, 2013 <DOI:10.1007/s13580-013-0140-9>), Taiwan Model (Lu et al., 2012 <DOI:10.17660/ActaHortic.2012.962.35>), Dynamic Model (Fishman et al., 1987, ISSN:0022-5193) adapted from the function Dynamic_Model() of the chillR package (Luedeling, 2018), Unified Model (Chuine et al., 2016 <DOI:10.1111/gcb.13383>) and Heat Restriction model.

Measuring child development starts by collecting responses to developmental milestones, such as "able to sit" or "says two words". There are many ways to combine such responses into summaries. The package bundles publicly available datasets with individual milestone data for children aged 0-5 years, with the aim of supporting the construction, evaluation, validation and interpretation of methodologies that aggregate milestone data into informative measures of child development.

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).

This package provides a database of Chinese surnames and Chinese given names (1930-2008). This database contains nationwide frequency statistics of 1,806 Chinese surnames and 2,614 Chinese characters used in given names, covering about 1.2 billion Han Chinese population (96.8% of the Han Chinese household-registered population born from 1930 to 2008 and still alive in 2008). This package also contains a function for computing multiple features of Chinese surnames and Chinese given names for scientific research (e.g., name uniqueness, name gender, name valence, and name warmth/competence).

This package provides functions to access data from the FINDIC API and the REST Countries API', related to Chile's financial indicators, international country information, and more. Additionally, the package includes curated datasets related to Chile, covering topics such as human rights violations during the Pinochet regime, electoral data, census samples, health surveys, seismic events, territorial codes, and environmental measurements. The package supports research and analysis focused on Chile by integrating open APIs with high-quality datasets from multiple domains. For more details on FINDIC', see <https://findic.cl/>, and for REST Countries', see <https://restcountries.com/>.

This package provides tools to extract word frequencies from the CHILDES (Child Language Data Exchange System) corpus. The main function allows users to input a list of words and receive speaker-role-specific frequency counts and a summary of the dataset. The output includes Excel-formatted tables of word counts and metadata summaries such as number of speakers, transcripts, children, and token counts. Useful for researchers studying early language acquisition, corpus linguistics, and speaker role variation. The CHILDES database is maintained at <https://childes.talkbank.org/>.

Perform post hoc analysis based on residuals of Pearson's Chi-squared Test for Count Data based on T. Mark Beasley & Randall E. Schumacker (1995) <doi: 10.1080/00220973.1995.9943797>.