LuyiTian/scPipe issues and pull requests

#100 - create_report() broken in devel

Issue - State: closed - Opened by PeteHaitch over 6 years ago - 2 comments

#99 - ERROR: compilation failed for package ‘scPipe’ in Centos7.3

Issue - State: closed - Opened by wenchuanxie over 6 years ago - 2 comments

#98 - Fixed sc_detect_bc returning one too many cell indices

Pull Request - State: closed - Opened by Shians over 6 years ago

#97 - Support for Sample Demultiplexing

Issue - State: closed - Opened by DarioS over 6 years ago - 2 comments

#96 - Added ability to use GRanges and data.frame as annotation

Pull Request - State: closed - Opened by Shians over 6 years ago

#95 - Disabled multiple BAM input for sc_exon_mapping

Pull Request - State: closed - Opened by Shians over 6 years ago - 5 comments

#94 - Error installing scPipe

Issue - State: closed - Opened by davetang over 6 years ago - 5 comments

#93 - Meaning of `UMI_cor = 2` in sc_gene_counting()

Issue - State: open - Opened by PeteHaitch over 6 years ago - 2 comments

#92 - Fix BC2_INFO__ in HTML report

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#91 - GO filter ID and other BioMart issues during calculate_QC_metrics()

Issue - State: open - Opened by okorn-src over 6 years ago - 1 comment

#90 - Ensure colData isn't clobbered by pheno_data in create_sce_by_dir()

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago

#89 - create_sce_by_dir() will error if passed a pheno_data

Issue - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#88 - Why do we need to respecify barcode information in sc_exon_mapping?

Issue - State: open - Opened by LTLA over 6 years ago - 4 comments

#87 - Support pre-loaded annotation data structures

Issue - State: open - Opened by LTLA over 6 years ago - 8 comments

#86 - Typo

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago

#85 - Document that output of sc_trim_barcode() can be automatically gzipped

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#84 - sc_demultiplex - barcode_match 0

Issue - State: closed - Opened by tkigih over 6 years ago - 2 comments

#83 - Multiple fastq files (multiple samples)

Issue - State: open - Opened by gk-bioin4m8x over 6 years ago - 5 comments

#82 - Updated README to use BiocManager

Pull Request - State: closed - Opened by Shians over 6 years ago

#81 - Updated get_read_str documentation

Pull Request - State: closed - Opened by Shians over 6 years ago

#80 - Convenience Parameter Specification for Popular Assays

Issue - State: open - Opened by DarioS over 6 years ago - 2 comments

#79 - Tidied up vignette

Pull Request - State: closed - Opened by Shians over 6 years ago

#78 - Vignette is Untidy

Issue - State: open - Opened by DarioS over 6 years ago

#77 - Corrected "suffix" argument in sc_detect_bc

Pull Request - State: closed - Opened by Shians over 6 years ago

#76 - Documentation update and optimisations

Pull Request - State: closed - Opened by Shians over 6 years ago - 2 comments

#75 - Possible logic error in Barcode::get_closest_match?

Issue - State: closed - Opened by Shians over 6 years ago - 1 comment

#74 - Added small parallelism to parse_align

Pull Request - State: closed - Opened by Shians over 6 years ago

#73 - Fixed R CMD CHECK errors

Pull Request - State: closed - Opened by Shians almost 7 years ago - 2 comments

#72 - Housekeeping changes

Pull Request - State: closed - Opened by Shians almost 7 years ago

#71 - ERCC counts missing

Issue - State: closed - Opened by Shians almost 7 years ago - 2 comments

#70 - Does distance to end of transcript make sense?

Issue - State: closed - Opened by Shians almost 7 years ago - 3 comments

#69 - Added tests, gzipped output and helper functions

Pull Request - State: closed - Opened by Shians almost 7 years ago

#68 - accept pre-demultiplexed files

Issue - State: closed - Opened by LuyiTian almost 7 years ago - 1 comment
Labels: enhancement, urgent

#67 - update the cell barcode demultiplex method

Issue - State: open - Opened by LuyiTian almost 7 years ago
Labels: enhancement

#66 - do not put all csv string in memory

Issue - State: open - Opened by LuyiTian almost 7 years ago - 4 comments
Labels: enhancement

#65 - Temporarily disabled reporting

Pull Request - State: closed - Opened by Shians almost 7 years ago

#64 - Fixed GeneBins implementation

Pull Request - State: closed - Opened by Shians almost 7 years ago

#63 - Rewrote gff parsing and gene counting

Pull Request - State: closed - Opened by Shians almost 7 years ago

#62 - Rewrite gff3 parser and read counting

Pull Request - State: closed - Opened by Shians almost 7 years ago - 1 comment

#61 - We should rethink is_outlier

Issue - State: open - Opened by Shians almost 7 years ago

#60 - segfault: Memory not mapped

Issue - State: open - Opened by MingBit almost 7 years ago - 3 comments

#59 - gencode GFF3 annotation sc_exon_mapping fault

Issue - State: open - Opened by ssmax1 almost 7 years ago - 14 comments

#58 - Fixed compilation bug on g++ 4.8.5

Pull Request - State: closed - Opened by Shians almost 7 years ago - 1 comment

#57 - Installation fails compiling C++ code "implicitly deleted because the default definition would be ill-formed"

Issue - State: open - Opened by lachlansimpson almost 7 years ago - 3 comments

#56 - Add org.Hs.eg.db and org.Mm.eg.db to import

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#55 - Release 3 6

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#54 - Release 3 6

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#53 - update release

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#52 - Fixed compiling error

Pull Request - State: closed - Opened by Shians about 7 years ago

#51 - Added prototype gzipped trim barcode functionality

Pull Request - State: closed - Opened by Shians about 7 years ago

#50 - Facilities for EntrezIDs

Issue - State: open - Opened by Shians about 7 years ago

#49 - Added count_aligned_bam wrapper function

Pull Request - State: closed - Opened by Shians about 7 years ago

#48 - Output gzipped fastq from trim barcode

Issue - State: open - Opened by Shians about 7 years ago - 1 comment

#47 - fix bug

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#46 - Release 3 6

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#45 - merge recent changes

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#44 - Need error tolerance for incorrect read structures

Issue - State: open - Opened by Shians about 7 years ago - 4 comments

#43 - Fixed bugs in slim report and trimbarcode error message

Pull Request - State: closed - Opened by Shians about 7 years ago

#42 - Fix incomplete error message

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#41 - Documentation updates, new functions and bug fixes

Pull Request - State: closed - Opened by Shians about 7 years ago - 1 comment

#40 - Release 3 6

Pull Request - State: closed - Opened by LuyiTian about 7 years ago

#39 - create_report fails if `outdir` is not the current directory

Issue - State: open - Opened by Shians about 7 years ago

#38 - sc_exon_mapping bam tag arguments

Issue - State: open - Opened by Shians about 7 years ago

#37 - Read structure handling

Issue - State: open - Opened by Shians about 7 years ago - 1 comment

#36 - Fixed handling of colData when assigning to QC_metrics

Pull Request - State: closed - Opened by Shians about 7 years ago

#35 - No R wrappers for 10X data processing?

Issue - State: closed - Opened by Shians about 7 years ago - 1 comment

#34 - Assigning to QC_metrics overrides colData

Issue - State: closed - Opened by Shians about 7 years ago - 2 comments

#33 - readr used in report template but not listed as a dependency

Issue - State: open - Opened by Shians over 7 years ago - 1 comment

#32 - Defaults on create_report inside create_sce_by_dir not sensible

Issue - State: closed - Opened by Shians over 7 years ago - 2 comments

#31 - Fixed bug when no QC_cols specified

Pull Request - State: closed - Opened by Shians over 7 years ago

#30 - Changed some checks and wording

Pull Request - State: closed - Opened by Shians over 7 years ago

#29 - Future

Pull Request - State: closed - Opened by LuyiTian over 7 years ago

#28 - scPipe loads a LOT of DLLs

Issue - State: closed - Opened by Shians over 7 years ago

#27 - ERROR: dependency ‘Rhtslib’ is not available for package ‘scPipe’

Issue - State: closed - Opened by steve-englart over 7 years ago - 4 comments

#26 - sc_demultiplex crashes R

Issue - State: closed - Opened by klprint over 7 years ago - 7 comments

#25 - Use official barcode and UMI tags

Issue - State: closed - Opened by Shians over 7 years ago

#24 - Fixed for Bioconductor

Pull Request - State: closed - Opened by Shians over 7 years ago

#23 - Added import(Rhtslib) to NAMESPACE

Pull Request - State: closed - Opened by Shians over 7 years ago

#22 - Added zlibbioc lines

Pull Request - State: closed - Opened by Shians over 7 years ago

#21 - detect_outlier per batch

Issue - State: closed - Opened by LuyiTian over 7 years ago

#20 - Updated report_template with new camelCase methods

Pull Request - State: closed - Opened by Shians over 7 years ago

#19 - Updated documentation

Pull Request - State: closed - Opened by Shians over 7 years ago

#18 - Changed code styling

Pull Request - State: closed - Opened by Shians over 7 years ago

#17 - BiocCheck FAILED

Issue - State: closed - Opened by LuyiTian over 7 years ago - 1 comment

#16 - finish the vignettes and add example data

Issue - State: closed - Opened by LuyiTian over 7 years ago

#15 - write convert function

Issue - State: closed - Opened by LuyiTian over 7 years ago

#14 - Trailing whitespace in sample annotation causes bug

Issue - State: closed - Opened by Shians over 7 years ago - 1 comment

#13 - 0 indexing on barcode and UMI indices

Issue - State: open - Opened by Shians over 7 years ago

#12 - Make function naming conventions consistent

Issue - State: closed - Opened by Shians over 7 years ago

#11 - Updated Makevars and Mclust arguments

Pull Request - State: closed - Opened by Shians over 7 years ago

#10 - Addressed some warnings

Pull Request - State: closed - Opened by Shians over 7 years ago

#9 - Removed some warnings

Pull Request - State: closed - Opened by Shians over 7 years ago

#8 - Added generic for organism

Pull Request - State: closed - Opened by Shians over 7 years ago

#7 - Fixed a lot of notes

Pull Request - State: closed - Opened by Shians over 7 years ago

#6 - Added imports and changed aes to aes_string

Pull Request - State: closed - Opened by Shians over 7 years ago

#5 - Added proper handling of type argument in detect_outlier

Pull Request - State: closed - Opened by Shians over 7 years ago

#4 - Added biocViews

Pull Request - State: closed - Opened by Shians over 7 years ago

#3 - go_id removed from biomaRt?

Issue - State: closed - Opened by LuyiTian almost 8 years ago

#2 - Changed barplot bar spacing

Pull Request - State: closed - Opened by Shians almost 8 years ago

#1 - Timings

Issue - State: closed - Opened by Shians almost 8 years ago

GitHub / LuyiTian/scPipe issues and pull requests