Title: Modelling and Forecasting Biological Invasions
Description: Analysing and forecasting biological invasions time series
with a stochastic, non mechanistic approach that gives proper weight
to the anthropic component, accounts for habitat suitability and
provides measures of precision for its estimates.
Packaged: 2017-02-02 17:07:13 UTC; lucabutikofer

with a stochastic, non-mechanistic approach that gives proper weight
Packaged: 2017-12-29 18:10:53 UTC; lucabutikofer

Description: Analysing and forecasting biological invasions time series with a stochastic approach that accounts for human-aided dispersal, habitat suitability and provides estimates confidence level.
Imports: raster (>= 2.5-2), fields (>= 8.3-6), spatstat.geom,
spatstat.core, spatstat (>= 2.0-0), sp (>= 1.2-4), grDevices
Packaged: 2021-03-29 18:54:29 UTC; lucabutikofer

Title: Paired (pBI) and Unpaired Biomarker Identifier (uBI) including a
Description: This package allows to rank features and infer networks
based on the Paired (pBI) and Unpaired Biomarker Identifier

Description: This package allows to rank features and infer networks based on the Paired (pBI) and Unpaired Biomarker Identifier (uBI).

Title: Identification of Impulse-Like Gene Expression Changes in Short
Description: Enables the user to systematically identify and visualize impulse-like gene expression changes within short genomic series experiments. In order to detect such activation peaks, the gene expression is treated as a signal that propagates along an experimental axis (time, temperature or other series conditions). Peaks are selected by exhaustive identification of local maximums and subsequent filtering based on a range of controllable parameters. Moreover, the 'Biopeak' package provides a series of data exploration tools including: expression profile plots, correlation heat maps and clustering functionalities.
Imports: cluster, dbscan, factoextra, gplots, RColorBrewer, stats,

Title: From Biological Sequences and Simulations to Correlation
Author: Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [cre]
Depends: R (>= 3.1), bio3d, circular, bigmemory, parallel
Description: The package is dedicated to computation and analysis of correlation/co-variation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the ability to compute correlation/co-variation using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and to analyze the correlation/co-variation matrix through a variety of tools including network representation and principal components analysis.  In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence co-variation analysis and utility tools are provided in: Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M. (2014) <doi:10.1002/prot.24570>. This work was supported by the Franch National Research Agency (Grant number: ANR-11-BSV2-026).