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  • Installation
  • API
    • DNA Module API Documentation
      • gcell.dna.motif.Motif
        • gcell.dna.motif.Motif.plot_logo
      • gcell.dna.motif.MotifCluster
        • gcell.dna.motif.MotifCluster.get_gene_name_list
      • gcell.dna.track.Track
        • gcell.dna.track.Track.conv_size
        • gcell.dna.track.Track.generate_bedgraph
        • gcell.dna.track.Track.generate_bigwig
        • gcell.dna.track.Track.get_local_iqr_peak
        • gcell.dna.track.Track.plot_tracks
        • gcell.dna.track.Track.plot_tracks_with_genebody
    • RNA Module API Documentation
      • gcell.rna.gencode.Gencode
        • gcell.rna.gencode.Gencode.DEFAULT_VERSIONS
        • gcell.rna.gencode.Gencode.gene_to_chrom
        • gcell.rna.gencode.Gencode.gene_to_id
        • gcell.rna.gencode.Gencode.gene_to_strand
        • gcell.rna.gencode.Gencode.gene_to_strand_numeric
        • gcell.rna.gencode.Gencode.gene_to_tes
        • gcell.rna.gencode.Gencode.gene_to_tss
        • gcell.rna.gencode.Gencode.gene_to_type
        • gcell.rna.gencode.Gencode.id_to_gene
        • gcell.rna.gencode.Gencode.original_gtf
        • gcell.rna.gencode.Gencode.from_config
        • gcell.rna.gencode.Gencode.get_exp_feather
        • gcell.rna.gencode.Gencode.get_gene
        • gcell.rna.gencode.Gencode.get_gene_id
        • gcell.rna.gencode.Gencode.get_genebodies
        • gcell.rna.gencode.Gencode.get_genes
        • gcell.rna.gencode.Gencode.query_region
      • gcell.rna.gtf.GTF
        • gcell.rna.gtf.GTF.get_exp_feather
        • gcell.rna.gtf.GTF.get_gene
        • gcell.rna.gtf.GTF.get_gene_id
        • gcell.rna.gtf.GTF.get_genebodies
        • gcell.rna.gtf.GTF.get_genes
        • gcell.rna.gtf.GTF.query_region
      • gcell.rna.gene.Gene
        • gcell.rna.gene.Gene.genomic_range
        • gcell.rna.gene.Gene.tes
        • gcell.rna.gene.Gene.tes_list
        • gcell.rna.gene.Gene.tss
        • gcell.rna.gene.Gene.tss_coordinate
        • gcell.rna.gene.Gene.get_tes_track
        • gcell.rna.gene.Gene.get_tes_track_obj
        • gcell.rna.gene.Gene.get_track
        • gcell.rna.gene.Gene.get_track_obj
        • gcell.rna.gene.Gene.get_tss_track
        • gcell.rna.gene.Gene.get_tss_track_obj
      • gcell.rna.gene.TSS
        • gcell.rna.gene.TSS.get_sample_from_peak
      • gcell.rna.gene.GeneExp
        • gcell.rna.gene.GeneExp.genomic_range
        • gcell.rna.gene.GeneExp.tes
        • gcell.rna.gene.GeneExp.tes_list
        • gcell.rna.gene.GeneExp.tss
        • gcell.rna.gene.GeneExp.tss_coordinate
        • gcell.rna.gene.GeneExp.get_tes_track
        • gcell.rna.gene.GeneExp.get_tes_track_obj
        • gcell.rna.gene.GeneExp.get_track
        • gcell.rna.gene.GeneExp.get_track_obj
        • gcell.rna.gene.GeneExp.get_tss_track
        • gcell.rna.gene.GeneExp.get_tss_track_obj
      • gcell.rna.gene.GeneSets
        • gcell.rna.gene.GeneSets.get_tss_track
    • Protein Module API Documentation
      • gcell.protein.get_seq_from_gene_name
      • gcell.protein.get_seq_from_uniprot_id
      • gcell.protein.get_lddt_from_gene_name
      • gcell.protein.get_lddt_from_uniprot_id
      • gcell.protein.get_uniprot_from_gene_name
      • gcell.protein.uniprot.UniProtAPI
        • gcell.protein.uniprot.UniProtAPI.batch_download_xml
        • gcell.protein.uniprot.UniProtAPI.download_database
        • gcell.protein.uniprot.UniProtAPI.download_xml
        • gcell.protein.uniprot.UniProtAPI.get_domains
        • gcell.protein.uniprot.UniProtAPI.get_protein_info
        • gcell.protein.uniprot.UniProtAPI.get_protein_sequence
        • gcell.protein.uniprot.UniProtAPI.get_uniprot_id
        • gcell.protein.uniprot.UniProtAPI.search_proteins
      • gcell.protein.af2.AFResult
      • gcell.protein.af2.AFMonomer
      • gcell.protein.af2.AFHomodimer
      • gcell.protein.af2.AFMultimer
      • gcell.protein.af2.AFPairseg
        • gcell.protein.af2.AFPairseg.plot_plddt_gene1
        • gcell.protein.af2.AFPairseg.plot_plddt_gene2
        • gcell.protein.af2.AFPairseg.plot_score_heatmap
        • gcell.protein.af2.AFPairseg.plotly_plddt_gene1
        • gcell.protein.af2.AFPairseg.plotly_plddt_gene2
    • Pathway Module API Documentation
      • gcell.ontology.pathway.Pathways
        • gcell.ontology.pathway.Pathways.get_gene_sets
        • gcell.ontology.pathway.Pathways.query_pathway
    • Celltype Module API Documentation
      • gcell.cell.celltype.Celltype
        • gcell.cell.celltype.Celltype.gene_by_motif
        • gcell.cell.celltype.Celltype.gene_jacobian_summary
        • gcell.cell.celltype.Celltype.get_gene_accessibility
        • gcell.cell.celltype.Celltype.get_gene_annot
        • gcell.cell.celltype.Celltype.get_gene_by_motif
        • gcell.cell.celltype.Celltype.get_gene_chromosome
        • gcell.cell.celltype.Celltype.get_gene_idx
        • gcell.cell.celltype.Celltype.get_gene_jacobian
        • gcell.cell.celltype.Celltype.get_gene_jacobian_summary
        • gcell.cell.celltype.Celltype.get_gene_obs
        • gcell.cell.celltype.Celltype.get_gene_pred
        • gcell.cell.celltype.Celltype.get_gene_strand
        • gcell.cell.celltype.Celltype.get_gene_tss
        • gcell.cell.celltype.Celltype.get_gene_tss_start
        • gcell.cell.celltype.Celltype.get_genes_exp
        • gcell.cell.celltype.Celltype.get_highest_exp_genes
        • gcell.cell.celltype.Celltype.get_input_data
        • gcell.cell.celltype.Celltype.get_tf_exp_mean
        • gcell.cell.celltype.Celltype.get_tf_exp_str
        • gcell.cell.celltype.Celltype.get_tf_pathway
        • gcell.cell.celltype.Celltype.get_tss_idx
        • gcell.cell.celltype.Celltype.get_tss_jacobian
        • gcell.cell.celltype.Celltype.load_gene_annot
        • gcell.cell.celltype.Celltype.plot_gene_motifs
        • gcell.cell.celltype.Celltype.plot_gene_regions
        • gcell.cell.celltype.Celltype.plot_region
        • gcell.cell.celltype.Celltype.plot_region_plotly
        • gcell.cell.celltype.Celltype.plotly_gene_exp
        • gcell.cell.celltype.Celltype.plotly_motif_subnet
      • gcell.cell.celltype.GETCellType
        • gcell.cell.celltype.GETCellType.gene_by_motif
        • gcell.cell.celltype.GETCellType.gene_jacobian_summary
        • gcell.cell.celltype.GETCellType.get_gene_accessibility
        • gcell.cell.celltype.GETCellType.get_gene_annot
        • gcell.cell.celltype.GETCellType.get_gene_by_motif
        • gcell.cell.celltype.GETCellType.get_gene_chromosome
        • gcell.cell.celltype.GETCellType.get_gene_idx
        • gcell.cell.celltype.GETCellType.get_gene_jacobian
        • gcell.cell.celltype.GETCellType.get_gene_jacobian_summary
        • gcell.cell.celltype.GETCellType.get_gene_obs
        • gcell.cell.celltype.GETCellType.get_gene_pred
        • gcell.cell.celltype.GETCellType.get_gene_strand
        • gcell.cell.celltype.GETCellType.get_gene_tss
        • gcell.cell.celltype.GETCellType.get_gene_tss_start
        • gcell.cell.celltype.GETCellType.get_genes_exp
        • gcell.cell.celltype.GETCellType.get_highest_exp_genes
        • gcell.cell.celltype.GETCellType.get_input_data
        • gcell.cell.celltype.GETCellType.get_tf_exp_mean
        • gcell.cell.celltype.GETCellType.get_tf_exp_str
        • gcell.cell.celltype.GETCellType.get_tf_pathway
        • gcell.cell.celltype.GETCellType.get_tss_idx
        • gcell.cell.celltype.GETCellType.get_tss_jacobian
        • gcell.cell.celltype.GETCellType.load_gene_annot
        • gcell.cell.celltype.GETCellType.plot_gene_motifs
        • gcell.cell.celltype.GETCellType.plot_gene_regions
        • gcell.cell.celltype.GETCellType.plot_region
        • gcell.cell.celltype.GETCellType.plot_region_plotly
        • gcell.cell.celltype.GETCellType.plotly_gene_exp
        • gcell.cell.celltype.GETCellType.plotly_motif_subnet
      • gcell.cell.celltype.GETHydraCellType
        • gcell.cell.celltype.GETHydraCellType.gene_by_motif
        • gcell.cell.celltype.GETHydraCellType.from_config
        • gcell.cell.celltype.GETHydraCellType.gene_jacobian_summary
        • gcell.cell.celltype.GETHydraCellType.get_gene_accessibility
        • gcell.cell.celltype.GETHydraCellType.get_gene_annot
        • gcell.cell.celltype.GETHydraCellType.get_gene_by_motif
        • gcell.cell.celltype.GETHydraCellType.get_gene_chromosome
        • gcell.cell.celltype.GETHydraCellType.get_gene_idx
        • gcell.cell.celltype.GETHydraCellType.get_gene_jacobian
        • gcell.cell.celltype.GETHydraCellType.get_gene_jacobian_region_norm
        • gcell.cell.celltype.GETHydraCellType.get_gene_jacobian_summary
        • gcell.cell.celltype.GETHydraCellType.get_gene_obs
        • gcell.cell.celltype.GETHydraCellType.get_gene_pred
        • gcell.cell.celltype.GETHydraCellType.get_gene_strand
        • gcell.cell.celltype.GETHydraCellType.get_gene_tss
        • gcell.cell.celltype.GETHydraCellType.get_gene_tss_start
        • gcell.cell.celltype.GETHydraCellType.get_genes_exp
        • gcell.cell.celltype.GETHydraCellType.get_highest_exp_genes
        • gcell.cell.celltype.GETHydraCellType.get_input_data
        • gcell.cell.celltype.GETHydraCellType.get_powerlaw_at_distance
        • gcell.cell.celltype.GETHydraCellType.get_tf_exp_mean
        • gcell.cell.celltype.GETHydraCellType.get_tf_exp_str
        • gcell.cell.celltype.GETHydraCellType.get_tf_pathway
        • gcell.cell.celltype.GETHydraCellType.get_tss_idx
        • gcell.cell.celltype.GETHydraCellType.get_tss_jacobian
        • gcell.cell.celltype.GETHydraCellType.load_gene_annot
        • gcell.cell.celltype.GETHydraCellType.plot_gene_motifs
        • gcell.cell.celltype.GETHydraCellType.plot_gene_regions
        • gcell.cell.celltype.GETHydraCellType.plot_region
        • gcell.cell.celltype.GETHydraCellType.plot_region_plotly
        • gcell.cell.celltype.GETHydraCellType.plotly_gene_exp
        • gcell.cell.celltype.GETHydraCellType.plotly_motif_subnet
  • Release notes
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    • Making a release
  • Current developers
  • References
  • .md

Contributing

Contributing#

Contributions to gcell are welcome! This section of the docs provides some guidelines and tips to follow when contributing.

  • Contributing code
    • Development workflow
    • Code style
  • Getting set up
    • Working with git
      • Forking and cloning
      • pre-commit
      • Creating a branch for your feature
      • Open a pull request
    • Development environments
  • Tests
    • Running the tests
      • Miscellaneous tips
    • Writing tests
      • What to test
      • Performance
      • Plotting tests
  • Documentation
    • Building the docs
    • Adding to the docs
    • docstrings format
      • Params section
      • Returns section
  • Versioning
    • Semantic versioning
      • Version numbers
    • Tooling
      • Technical details
  • Making a release
    • Preparing the release
    • Actually making the release
    • After making a release
    • Debugging the build process

Parts of the guidelines have been adapted from the pandas and MDAnalysis guides. These are both excellent guides and we highly recommend checking them out.

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By gcell development team

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