modules

  • cell_ranger

    • count

      Quantify gene expression in a single cell RNA-seq dataset.

      • mkref

        Creates an index for use with Cell Ranger. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

      • cell_ranger_arc

        • count

          Aligns and quantifies FastQ files from a 10X snRNA+ATAC-seq experiment against a reference genome. Output matrices are provided in triplet and h5 formats.

          • make_libraries_csv

            Creates a sample sheet for a whole project, listing the sample names, assay types and paths to FastQ files. It can be subset to produce a sample sheet for a sample.

            • mkref

              Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

            • cell_ranger_multi

              • count

                Aligns and quantifies FastQ files from a multiomic 10x experiment against a reference genome and include VDJ-B/T and cell surface markers. Output matrices for gene expression and features are provided in triplet and h5 formats. VDJ data are provided separately.

                • make_input_csv

                  Creates a configuration file for a library, listing the sample names, assay types and paths to FastQ files (etc).

                • R

                • samtools

                  • faidx

                    Create a FastA index from a FastA file, providing a `.fai` file.

                  • tools

                    • cat

                      Concatenate multiple files into a single output file. Different input formats can be used; based on the extension, YAML files are concatenated using `yq`, otherwise `cat` is used.

                    Subsections of modules

                    cell_ranger

                    • count

                      Quantify gene expression in a single cell RNA-seq dataset.

                      • mkref

                        Creates an index for use with Cell Ranger. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

                        Subsections of cell_ranger

                        cell_ranger_arc

                        • count

                          Aligns and quantifies FastQ files from a 10X snRNA+ATAC-seq experiment against a reference genome. Output matrices are provided in triplet and h5 formats.

                          • make_libraries_csv

                            Creates a sample sheet for a whole project, listing the sample names, assay types and paths to FastQ files. It can be subset to produce a sample sheet for a sample.

                            • mkref

                              Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

                              Subsections of cell_ranger_arc

                              cell_ranger_multi

                              • count

                                Aligns and quantifies FastQ files from a multiomic 10x experiment against a reference genome and include VDJ-B/T and cell surface markers. Output matrices for gene expression and features are provided in triplet and h5 formats. VDJ data are provided separately.

                                • make_input_csv

                                  Creates a configuration file for a library, listing the sample names, assay types and paths to FastQ files (etc).

                                  Subsections of cell_ranger_multi

                                  R

                                  Subsections of R

                                  biomaRt

                                  • get_mart

                                    Make a connection to the release-matched Ensembl database and saves the object as an RDS file.

                                    Subsections of biomaRt

                                    GenomeInfoDB

                                    • convert_fai_to_seqinfo

                                      Converts a FastA index (`fai`) to a {GenomeInfoDb} `Seqinfo` object and saves the object to an RDS file.

                                      Subsections of GenomeInfoDB

                                      GenomicRanges

                                      Subsections of GenomicRanges

                                      Seurat

                                      • make_assay

                                        Writes assay objects as RDS files for a specified assay type.

                                        • make_object

                                          A Seurat object is created from the assays, metadata and miscellaneous objects and written to an RDS file.

                                          • percentage_feature_set

                                            Adds a metadata variable that shows the perentage of a cell's data that originates from features that match a regex.

                                            • write_10x_counts_matrices

                                              Reads a directory containing Cell Ranger-formatted output into a list of matrices.

                                              Subsections of Seurat

                                              Subsections of Signac

                                              samtools

                                              • faidx

                                                Create a FastA index from a FastA file, providing a `.fai` file.

                                                Subsections of samtools

                                                tools

                                                • cat

                                                  Concatenate multiple files into a single output file. Different input formats can be used; based on the extension, YAML files are concatenated using `yq`, otherwise `cat` is used.

                                                  Subsections of tools

                                                  cat