Dev #173
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Dev #173
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Chenjunjie1996
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Dec 14, 2022
* tested * lint * refactor * update EBV * change to markdown * Dev (#167) * fix merge_table and other parameter Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> * change to md * typo * Update snp_v.1.5.1.md * update * print args * `Reads without poly T` are not filtered by default. * remove chinese in logo * rm `allowNoPolyT` in docs * add split_fl_vdj in tag assay (#170) Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> * add cr-count in convert_10X (#171) * get_seq_str Raise IndexError: if sequence length is not enough * add rna_virus * Dev (#173) * add split_fl_vdj in tag assay * add cr-count in convert10X * output filter_contig_annotation.csv * merge convert and add 10X chemistry option Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> * include intron reads by default * Add an argument `--mixcr_mem` * bump version 1.12.0b0 * utils assay (#175) * add split_fl_vdj in tag assay * add cr-count in convert10X * output filter_contig_annotation.csv * merge convert and add 10X chemistry option * celescope mkgtf * celescope mkgtf * lint * add utils assay * lint * lint Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> Co-authored-by: 陈俊杰 <chenjunjie@SGRNJshiny.sgr.com> * fix mapping tag * update changelog;bump version 1.12.0 * refactor mkgtf * lint * fix matplotlib version * bump version 1.12.1 * init * tested * update * tested * acc html (#180) * acc html * fix * pylint * allow no space after semicolon in gtf 9th column * add docs * lint * update docs * add sweetseq to multi * If two or more groups of reads have the same barcode and UMI, but different gene annotations, the gene annotation with the most supporting reads is kept for UMI counting, and the other read groups are discarded. In case of a tie for maximal read support, all read groups are discarded, as the gene cannot be confidently assigned. * refactor * fix argparse help error * Fix genes without gene annotation * bump version; update changelog and docs * Dev (#190) * output fl metrics for each tag Co-authored-by: 陈俊杰 <chenjunjie@SGRNJshiny.sgr.com> * init * Dev (#196) * update cr7.0 version Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> * 1.14.0b0 * pylint * Dev (#202) * add split_fl_vdj in tag assay * add cr-count in convert10X * output filter_contig_annotation.csv * merge convert and add 10X chemistry option * celescope mkgtf * celescope mkgtf * lint * add utils assay * lint * lint * output fl metrics for each tag * update cr7.0 version * igblast vdj * refactor vdj * update docs * fix * fix * fix * fix * lint * conda install igblast, add mkref command * update docs * fix * lint * replace CDR3 with rearrangement's junction (CDR3) * add bcr docs Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> Co-authored-by: 陈俊杰 <chenjunjie@SGRNJshiny.sgr.com> * CDR3 vdj ref * add transcript name if snp is not on exon * bump version v1.14.0b0 * use 'pip install scikit-learn' rather than 'pip install sklearn' * change python-version to 3.9 in release.yml * fix igblast install Co-authored-by: zhouyiqi <zhouyiqi@singleronbio.com> Co-authored-by: 陈俊杰 <chenjunjie@SGRNJlogin.sgr.com> Co-authored-by: 陈俊杰 <chenjunjie@SGRNJshiny.sgr.com> Co-authored-by: wuqi21 <68728396+wuqi21@users.noreply.github.com>
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out put filter_contig_annotation.csv
merge convert module
add 10X chemistry option