├── .gitignore ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── alignqc ├── __init__.py ├── alignqc.py ├── analyze.py ├── annotate_from_genomic_features.py ├── annotated_length_analysis.py ├── annotated_read_bias_analysis.py ├── bam_preprocess.py ├── bam_to_alignment_error_plot.py ├── bam_to_chr_lengths.py ├── bam_to_context_error_plot.py ├── compare.py ├── create_html.py ├── data │ └── mystyle.css ├── depth_to_coverage_report.py ├── dump.py ├── get_depth_subset.py ├── get_platform_report.py ├── gpd_annotation_to_rarefraction.py ├── gpd_loci_analysis.py ├── gpd_to_exon_distro.py ├── gpd_to_junction_variance.py ├── locus_bed_to_rarefraction.py ├── make_alignment_plot.py ├── make_solo_html.py ├── plot_alignment_errors.r ├── plot_annotated_features.r ├── plot_annotation_analysis.r ├── plot_annotation_rarefractions.r ├── plot_base_error_context.r ├── plot_bias.r ├── plot_chr_depth.r ├── plot_depthmap.r ├── plot_exon_distro.r ├── plot_feature_depth.r ├── plot_gapped_alignment_statistics.r ├── plot_junvar.r ├── plot_pacbio.r ├── plot_transcript_lengths.r ├── prepare_all_data.py └── traverse_preprocessed.py ├── example_data ├── chr21chr22chrM.bam ├── chr21chr22chrM.fa.gz ├── chr21chr22chrM.gencode25.gpd.gz └── chr21chr22chrM.gencode25.gtf.gz ├── meta.yaml ├── scripts ├── alignqc_annotation_to_bed_depth.py ├── alignqc_to_novel_transcriptome.py ├── alignqcs_to_read_lengths.py ├── alignqcs_to_read_type_count_per_cell_statistics.py └── classify_reads.py ├── setup.py └── tests └── __init__.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jason-weirather/AlignQC/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jason-weirather/AlignQC/HEAD/Dockerfile 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