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.