Showing 9 of total 9 results (show query)
ts404
WikidataR:Read-Write API Client Library for Wikidata
Read from, interrogate, and write to Wikidata <https://www.wikidata.org> - the multilingual, interdisciplinary, semantic knowledgebase. Includes functions to: read from Wikidata (single items, properties, or properties); query Wikidata (retrieving all items that match a set of criteria via Wikidata SPARQL query service); write to Wikidata (adding new items or statements via QuickStatements); and handle and manipulate Wikidata objects (as lists and tibbles). Uses the Wikidata and QuickStatements APIs.
Maintained by Thomas Shafee. Last updated 3 months ago.
22 stars 9.01 score 109 scripts 28 dependents
eco-hydro
phenofit:Extract Remote Sensing Vegetation Phenology
The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>; Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636. <doi:10.1029/2020JG005636>; Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24; Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Maintained by Dongdong Kong. Last updated 2 months ago.
phenologyremote-sensingopenblascppopenmp
78 stars 7.71 score 332 scripts
statisticsnorway
SSBtools:Algorithms and Tools for Tabular Statistics and Hierarchical Computations
Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Maintained by Øyvind Langsrud. Last updated 19 days ago.
7 stars 7.62 score 68 scripts 7 dependents
bioc
syntenet:Inference And Analysis Of Synteny Networks
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
Maintained by Fabrício Almeida-Silva. Last updated 4 months ago.
softwarenetworkinferencefunctionalgenomicscomparativegenomicsphylogeneticssystemsbiologygraphandnetworkwholegenomenetworkcomparative-genomicsevolutionary-genomicsnetwork-sciencephylogenomicssyntenysynteny-networkcpp
28 stars 6.70 score 12 scripts 1 dependents
mottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 6 months ago.
5 stars 6.39 score 41 scripts
luomus
fbi:Finnish Biodiversity Indicators
Finnish biodiversity indicators is a service providing time series of abundance indices and related metrics for Finland. The input data for the indices are provided by the Finnish Biodiversity Information Facility.
Maintained by William K. Morris. Last updated 9 days ago.
5.89 score 60 scripts
barcaroli
R2BEAT:Multistage Sampling Allocation and Sample Selection
Multivariate optimal allocation for different domains in one and two stages stratified sample design. 'R2BEAT' extends the Neyman (1934) – Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethel’s proposal (1989). 'R2BEAT' develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples. It also allows to perform both Primary Stage Units and Secondary Stage Units selection. This package requires the availability of 'ReGenesees', that can be installed from <https://github.com/DiegoZardetto/ReGenesees>.
Maintained by Andrea Fasulo. Last updated 3 months ago.
2 stars 4.62 score 35 scriptsbioc
rifi:'rifi' analyses data from rifampicin time series created by microarray or RNAseq
'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.
Maintained by Jens Georg. Last updated 5 months ago.
rnaseqdifferentialexpressiongeneregulationtranscriptomicsregressionmicroarraysoftware
4.60 score 1 scripts
