Catoni, M., Tsang, J. M. F., Greco, A. P. & Zabet, N. R. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.
The formats of input and output files and the availability of sample datasets are summarized in Table 3. PowerGet is a standalone Java software package for detection, alignment, and annotation of metabolite features from data obtained using LC-high-resolution-MS (HRMS).
In The Lancet's Stillbirth Series, Bhutta et al. [ 31] identified a package of 10 interventions during pregnancy and childbirth to prevent stillbirths globally, including expanded antenatal care packages for improved detection and management of hypertension and diabetes in pregnancy, improved detection of high risk pregnancies and fetal compromise, and induction of labor after 41 weeks gestation.
Popular software packages for automated detection and classification include ISHMAEL (Mellinger, 2001), PAMGUARD (Gillespie et al., 2008), and XBAT (Figueroa, 2011).
HHsearch is a software package for the detection of remotely related protein sequences based on the pairwise comparison of HMMs.
We present readDepth, a new R package for CNA detection that does not require the sequencing of matched normal sample.
Finally, CHiCAGO is an open-source R package for interaction detection in CHi-C datasets.
To complement the variant calls from currently available tools we developed a novel software package for the detection and annotation of germline and somatic variants in RRA loci that we named RAREVATOR (RAre REference VAriant annotaTOR).
Here, we present CAFE Chromosomal Aberration Finder in Expression data as an R package for the detection of gross chromosomal gains and losses from expression microarrays, with a resolution up to cytoband level.
The data were filtered for absent genes by applying the MAS5 algorithm implemented in the Bioconductor affy package (version 1.22.1) for detection of present calls.
