Half-Normal Plots with Simulation Envelopes
lme4, gamlss, gamlss.dist, pscl, nnet, aods3, VGAM, glmmADMB,
latticeExtra
Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.

Various functions for higher order likelihood-based
inference

R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
graphics, statmod, stats, survival, utils
Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions  of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).

Information retrieval from NCBI databases, with main focus on Blast.

Information Retrieval for Genetic Datasets
c(person(given = "Daniel", family = "Fischer", role = c("aut","cre"), email = "daniel.fischer@luke.fi"),
person(given = "Anu", family = "Sironen", role = "aut"))
Daniel Fischer [aut, cre],
Anu Sironen [aut]
Information retrieval from National Center for Biotechnology Information (NCBI) databases, with main focus on identifying genes in unannotated organisms via Blast similarity search in annotated organisms.

Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices
Daniel Fischer [aut, cre], Anu Sironen [aut]
httr (>= 0.2), XML (>= 3.98-1.1), stringr (>= 0.6.2), MASS (>=
7.3-31), R.utils (>= 1.32.4), data.table, seqinr, Biostrings,
GenomicRanges, bamsignals, IRanges, Rsamtools, RCurl,
GenomicTools (>= 0.2.1)
Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.

Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Web Services
httr (>= 0.2), XML (>= 3.98-1.1), stringr (>= 0.6.2), MASS (>=
7.3-31), R.utils (>= 1.32.4), data.table, seqinr, Biostrings,
GenomicRanges, bamsignals, IRanges