Changes in version 1.3.13 (2018-10-22): o fixed bug in `create_report()` due to `changes` in scater parameters Changes in version 1.3.11: o added `get_ercc_anno()` function to retrieve ERCC annotation as data.frame o fixed `sc_detect_bc()` returning one more cell than requested Changes in version 1.3.10: o added option to use GRanges objects as annotation o added option to use SAF formatted data.frame objects as annotation o added support for gzipped annotation files Changes in version 1.3.8: o fix a minor bug in cell barcode demultiplexing o corrected `suffix` argument in `sc_detect_bc` to `prefix` Changes in version 1.3.7: o added multithreading to `parse_align` o added nthreads argument to `parse_align` and all upstream wrappers Changes in version 1.3.6: o support multiple bam file for the same sample pooling as input for exon mapping Changes in version 1.3.5: o bug fix Changes in version 1.3.4: o put `distance_to_end` back. Changes in version 1.3.2: o Added gzipped output for `sc_trim_barcode()`, if output filename ends with `.gz` then gzipped output will be produced. o Added `get_read_str()` function for getting common read structures. Changes in version 1.3.1: o updated the `sc_exon_mappping` function so it can accept multiple bam files now, together with a list of cell id or cell barcode. Changes in version 1.1.4: o improved the `sc_detect_bc` function. add white list which is a list of known 10x barcode also added a new argument `number_of_cells` to limit the maximum number of cell barcodes in the result. Changes in version 1.1.0-1.1.3: o fix the bugs that related to the reimplementation of the exon mapping algorithm Changes in version 1.0.9: o fix the bug that might misalign the exon mapping reads o support gff files from gencode or refseq Changes in version 1.0.8: o update the gene id annotation code Changes in version 1.0.6 (2017-12-18): o Now the id conversion can also be done by using the bioconductor annotation package, when biomart fails to connect. Changes in version 1.0.5 (2017-12-14): o Fixed bugs in slim report and trimbarcode error message o Fix incomplete error message o Documentation updates, new functions and bug fixes Changes in version 1.0.4 (2017-12-04): o In `detect_outlier`, give more informative error message when some cells or QC metrics have zero values. Changes in version 1.0.3 (2017-12-03): o fix a bug in `validObject`. the default value for gene id and organism is set to NA Changes in version 1.0.2 (2017-12-01): o fix errors in unittest Changes in version 1.0.1 (2017-11-28): o Bug Fix: Fixed handling of colData through QC_metrics (https://github.com/LuyiTian/scPipe/issues/34) Changes in version 0.99.20 (2017-09-22): o scPipe now supports SingleCellExperiment class and use it as the base class o add two functions `plot_demultiplex` and `plot_UMI_dup` o scPipe support the offical bam tags for cell barcode and UMI Changes in version 0.99.0 (2017-07-28): o Package prepared for Bioconductor submission.