NEWS

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scPipe 1.9.4 (2020-04-06)

• Changed hashmap package calls to hash package as hashmap is no longer on CRAN.

scPipe 1.9.1 (2019-12-23)

• Changed instances of deprecated 'plotQC()' to 'plotHighestExprs()'

scPipe 1.5.2 (2018-12-18)

• 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.

scPipe 1.3.16 (2018-10-31)

• add travis integration and codecov report.

• fixed broken examples

scPipe 1.3.13 (2018-10-22)

• fixed bug in 'create_report()' due to 'changes' in scater parameters

scPipe 1.3.11

• added 'get_ercc_anno()' function to retrieve ERCC annotation as data.frame

• fixed 'sc_detect_bc()' returning one more cell than requested

scPipe 1.3.10

• added option to use GRanges objects as annotation

• added option to use SAF formatted data.frame objects as annotation

• added support for gzipped annotation files

scPipe 1.3.8

• fix a minor bug in cell barcode demultiplexing

• corrected 'suffix' argument in 'sc_detect_bc' to 'prefix'

scPipe 1.3.7

• added multithreading to 'parse_align'

• added nthreads argument to 'parse_align' and all upstream wrappers

scPipe 1.3.6

• support multiple bam file for the same sample pooling as input for exon mapping

scPipe 1.3.5

• bug fix

scPipe 1.3.4

• put 'distance_to_end' back.

scPipe 1.3.2

• Added gzipped output for 'sc_trim_barcode()', if output filename ends with '.gz' then gzipped output will be produced.

• Added 'get_read_str()' function for getting common read structures.

scPipe 1.3.1

• updated the 'sc_exon_mappping' function so it can accept multiple bam files now, together with a list of cell id or cell barcode.

scPipe 1.1.4

• 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.

scPipe 1.1.0-1.1.3

• fix the bugs that related to the reimplementation of the exon mapping algorithm

scPipe 1.0.9

• fix the bug that might misalign the exon mapping reads

• support gff files from gencode or refseq

scPipe 1.0.8

• update the gene id annotation code

scPipe 1.0.6 (2017-12-18)

• Now the id conversion can also be done by using the bioconductor annotation package, when biomart fails to connect.

scPipe 1.0.5 (2017-12-14)

• Fixed bugs in slim report and trimbarcode error message

• Fix incomplete error message

• Documentation updates, new functions and bug fixes

scPipe 1.0.4 (2017-12-04)

• In 'detect_outlier', give more informative error message when some cells or QC metrics have zero values.

scPipe 1.0.3 (2017-12-03)

• fix a bug in 'validObject'. the default value for gene id and organism is set to NA

scPipe 1.0.2 (2017-12-01)

• fix errors in unittest

scPipe 1.0.1 (2017-11-28)

• Bug Fix: Fixed handling of colData through QC_metrics (https://github.com/LuyiTian/scPipe/issues/34)

scPipe 0.99.20 (2017-09-22)

• scPipe now supports SingleCellExperiment class and use it as the base class

• add two functions 'plot_demultiplex' and 'plot_UMI_dup'

• scPipe support the offical bam tags for cell barcode and UMI

scPipe 0.99.0 (2017-07-28)

• Package prepared for Bioconductor submission.