```{r setup，echo = false}库（usebiocumon）stopifnot（Biocinstaller :: biocversion（）==“3.1”）``````{r styce，echo = false，结果='asis'}生物焦:: markdown（）```＃新和相关包马丁摩根
2015年2月3日## _BIOcidodder_包`R biocpkg（“genomicfiles”）` - `genomicfiles（）`，与Intereset地区协调磁盘文件--`dreamby *（）`以迭代区域或文件 - `reduceByYield()` to iterate through files, e.g., `BamFile(..., yieldSize=1000000)` `r Biocpkg("GenomeInfoDb")` - Manipulate `seqlevels()`, e.g., keep only standard chromsomes (`keepStandardChromosomes()`), place in standard order (`sortSeqlevels()`), rename (`renameSeqlevels()`) `r Biocpkg("BiocStyle")` - Standardize formatting - HTML vignettes _much_ more usable than PDF - Supports `rmarkdown` (`Rhtslib`) ## _Bioconductor_ functionality `GenomicAlignments::readGAlignmentPairs()` / `readGAlignmentsList()` `Rsamtools::pileup()` `VariantAnnotation::VRanges()` `findOverlaps()`: significant performance improvements `AnnotationDbi::mapIds()` ## Contributed packages `r Biocpkg("csaw")` - Quantitative variation in ChIP binding; differential binding between treatment groups more relevant binding _per se_. - See the _Bioconductor_ [newsletter](//www.andersvercelli.com/help/newsletters/2015_January/#overview-of-the-csaw-package), especially final question for statistical rationale and advanced implementation (very interesting reading). `r Biocpkg("Rariants")` - SNVs from comparative shifts in non-consensus base call frequencies. `r Biocpkg("SGSeq")` - Prediction, quantification and visualization of alternative transcript events (rather than assessment of whole-transcript abundance). `r Biocpkg("ballgown")` - differential expression of assembled transcriptomes, `r Biocpkg("derfinder")` - base-level differential expression `r Biocpkg("AnalysisPageServer")` - interactive reports(!) `r Biocpkg("ggtree")` - Impressive visualization of phylogenetic trees ## Etc. - [New packages](//www.andersvercelli.com/developers/new_packages/) summary (also posted to twitter)