annotation_to_fasta | GTF/GFF to FASTA conversion |
blaze | BLAZE Assign reads to cell barcodes. |
bulk_long_pipeline | Pipeline for Bulk Data |
combine_sce | Combine SCE |
create_config | Create Configuration File From Arguments |
create_sce_from_dir | Create 'SingleCellExperiment' object from 'FLAMES' output folder |
create_se_from_dir | Create 'SummarizedExperiment' object from 'FLAMES' output folder |
cutadapt | cutadapt wrapper |
demultiplex_sockeye | Demultiplex reads using Sockeye outputs |
filter_annotation | filter annotation for plotting coverages |
find_barcode | Match Cell Barcodes |
find_isoform | Isoform identification |
find_variants | bulk variant identification |
FLAMES | FLAMES: full-length analysis of mutations and splicing |
flexiplex | Rcpp port of flexiplex |
get_GRangesList | Parse FLAMES' GFF output |
minimap2_align | Minimap2 Align to Genome |
minimap2_realign | Minimap2 re-align reads to transcriptome |
parse_gff_tree | Parse Gff3 file |
plot_coverage | plot read coverages |
plot_demultiplex | Plot Cell Barcode demultiplex statistics |
quantify_gene | Gene quantification |
quantify_transcript | Transcript quantification |
scmixology_lib10 | scMixology short-read gene counts - sample 2 |
scmixology_lib10_transcripts | scMixology long-read transcript counts - sample 2 |
scmixology_lib90 | scMixology short-read gene counts - sample 1 |
sc_DTU_analysis | FLAMES Differential Transcript Usage Analysis |
sc_heatmap_expression | FLAMES heetmap plots |
sc_long_multisample_pipeline | Pipeline for Multi-sample Single Cell Data |
sc_long_pipeline | Pipeline for Single Cell Data |
sc_mutations | Variant count for single-cell data |
sc_reduce_dims | runPCA and runUMAP wrapper |
sc_umap_expression | FLAMES UMAP plots |
sys_which | Sys.which wrapper Wrapper for Sys.which that replaces "" with NA |