The "partially overlapping samples t-tests", for the comparison
of means for two samples which include both paired observations and independent
observations. [See Derrick, B., Russ, B., Toher, D. & White P (2017). Test
statistics for the comparison of means for two samples which include both paired
observations and independent observations. Journal of Modern Applied Statistical
Methods, 16(1)].

Tests for a comparison of two partially overlapping samples.
A comparison of means using the partially overlapping samples t-test:
See Derrick, Russ, Toher and White (2017), Test
statistics for the comparison of means for two samples which include
both paired observations and independent observations, Journal of
Modern Applied Statistical Methods, 16(1).
A comparison of proportions using the partially overlapping samples z-test:
See Derrick, Dobson-Mckittrick, Toher and White (2015), Test statistics
for comparing two proportions with partially overlapping samples.
Journal of Applied Quantitative Methods, 10(3).

Preprocessing of Aligned Sequences from HTS Analyses
Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
bitops, tools, methods, S4Vectors, IRanges, GenomicRanges,
ShortRead, Rsamtools, Biostrings, gtools
R (>= 3.2.0), parallel, GenomicAlignments
ChIPSeq, Sequencing, Software, Preprocessing, Alignment

Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe Andrau
bitops, tools, methods, S4Vectors, IRanges, GenomicRanges,
ShortRead, Rsamtools, Biostrings, gtools, rtracklayer,
GenomeInfoDb