Changes in version 1.9.4 (2020-04-06) o Changed hashmap package calls to hash package as hashmap is no longer on CRAN. Changes in version 1.9.1 (2019-12-23) o Changed instances of deprecated `plotQC()` to `plotHighestExprs()` Changes in version 1.5.2 (2018-12-18) o add new function `sc_correct_bam_bc`, which will update the cell barcode tag in bam file with corrected barcode, using existing cell barcode annotation. Changes in version 1.3.16 (2018-10-31) o add travis integration and codecov report. o fixed broken examples 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.