AIRR tutorial

.gitignore

@@ -2,4 +2,4 @@
 build
 .history
 build
-**/.DS_Store
+**/.DS_Store.DS_Store

README.md

@@ -16,6 +16,7 @@ For installation instructions, please check the [documentation](https://github.c
 - [Ingesting MERFISH data with Panpipes](docs/ingesting_merfish_data/Ingesting_merfish_data_with_panpipes.md)  
 - [Filtering and preprocessing spatial data with Panpipes](docs/preprocess_spatial_data/preprocess_spatial_data_with_panpipes.md)
 - [Deconvoluting spatial data with Panpipes](docs/deconvolution/deconvoluting_spatial_data_with_panpipes.md)
+- [Analyzing scRNA-seq and scTCR-seq Data with Panpipes](docs/ingesting_airr_data/ingesting_airr_data.md)
 - [Contributing to Panpipes](docs/contributing.md) 
 
 

docs/index.md

@@ -11,6 +11,7 @@ For installation please check the [documentation](https://panpipes-pipelines.rea
 ingesting_data/Ingesting_data_with_panpipes.md
 ingesting_multiome/ingesting_mome.md
 ingesting_multimodal_data/ingesting_multimodal_data.md
+ingesting_airr_data/ingesting_airr_data.md
 ingesting_mouse/Ingesting_mouse_data_with_panpipes.md
 filtering_data/filtering_data_with_panpipes.md
 uni_multi_integration/Integrating_data_with_panpipes.md

docs/ingesting_airr_data/files/pipeline.yml

@@ -0,0 +1,182 @@
+# ============================================================
+# Ingest workflow Panpipes (pipeline_ingest.py)
+# ============================================================
+# This file contains the parameters for the ingest workflow.
+# For full descriptions of the parameters, see the documentation at https://panpipes-pipelines.readthedocs.io/en/latest/yaml_docs/pipeline_ingestion_yml.html
+
+#--------------------------
+# Compute resources options
+#--------------------------
+resources:
+  threads_high: 1
+  threads_medium: 1
+  threads_low: 1
+
+condaenv:
+
+# --------------------------------
+# Loading and merging data options
+# --------------------------------
+
+# ----------------------------
+# Project name and data format
+project: "vdjtest"
+sample_prefix: "vdjtest"
+use_existing_h5mu: False
+submission_file: ../short_vdj_submission.tsv
+metadatacols: sample_id,disease_state,tissue,preservation_method,celltype
+concat_join_type: inner
+
+#--------------------------
+# Modalities in the project
+modalities:
+  rna: True
+  prot: False
+  bcr: True
+  tcr: True
+  atac: False
+
+#--------------------------------
+# Integrating barcode level data
+# e.g. demultiplexing with hashtags, chemical tags or lipid tagging
+barcode_mtd:
+  include: False
+  path:
+  metadatacols:
+
+#------------------------------------------
+# Loading Protein data - additional options
+protein_metadata_table:
+index_col_choice:
+load_prot_from_raw: False
+subset_prot_barcodes_to_rna: False
+
+# -----------------------------
+# Quality Control (QC) options
+# -----------------------------
+
+# -----------------------------------
+# Processing of 10X cellranger metrics files
+plot_10X_metrics: True
+
+# ----------------------------------
+# Doublet detection on RNA modality
+scr:
+  run: True
+  expected_doublet_rate: 0.06
+  sim_doublet_ratio: 2
+  n_neighbours: 20
+  min_counts: 2
+  min_cells: 3
+  min_gene_variability_pctl: 85
+  n_prin_comps: 30
+  use_thr: True
+  call_doublets_thr: 0.25
+
+# ----------------------------
+# RNA modality Quality Control
+
+# Providing a gene list
+# see documentation at https://panpipes-pipelines.readthedocs.io/en/latest/usage/gene_list_format.html
+custom_genes_file: qc_genelist_1.0.csv
+
+# Defining actions on the genes
+
+# (for pipeline_ingest.py)
+calc_proportions: hb,mt,rp
+score_genes:
+
+# cell cycle action
+ccgenes: default
+
+# ------------------------
+# Plotting RNA QC metrics
+# all metrics should be provided as a comma separated string e.g. a,b,c
+# plotqc_grouping_var: orig.ident
+plotqc_grouping_var: sample_id
+plotqc_rna_metrics: doublet_scores,pct_counts_mt,pct_counts_rp,pct_counts_hb,pct_counts_ig
+
+# ----------------------------
+# Plotting Protein QC metrics
+
+# requires prot_path to be included in the submission file
+# all metrics should be provided as a comma separated string e.g. a,b,c
+plotqc_prot_metrics: total_counts,log1p_total_counts,n_prot_by_counts,pct_counts_isotype
+plot_metrics_per_prot: total_counts,log1p_total_counts,n_cells_by_counts,mean_counts
+
+identify_isotype_outliers: True
+isotype_upper_quantile: 90
+isotype_n_pass: 2
+
+# ---------------------
+# Plot ATAC QC metrics
+
+# set is_paired to True if a multiome is ingested
+is_paired: True
+# If this is NOT a multiome experiment, but you have an RNA anndata that you would like to use for TSS enrichment
+# use the partner_rna to specify the path to the file and provide a features_tss file with the tss coordinates
+# leave empty if multiome is used
+partner_rna:
+features_tss:
+plotqc_atac_metrics: n_genes_by_counts,total_counts,pct_fragments_in_peaks,atac_peak_region_fragments,atac_mitochondrial_reads,atac_TSS_fragments
+
+# ---------------------------
+# Plot Repertoire QC metrics
+ir_dist:
+  metric:
+  sequence:
+
+clonotype_definition:
+  receptor_arms:
+  dual_ir:
+  within_group:
+
+plotqc_rep_metrics:
+  # provide a item list
+  - is_cell
+  - extra_chains
+  - clonal_expansion
+  - rep:receptor_type
+  - rep:receptor_subtype
+  - rep:chain_pairing
+  - rep:multi_chain
+
+# -------------------------------------
+# Profiling Protein Ambient background
+# -------------------------------------
+# PLEASE NOTE that this analysis can only be run if your inputs are from cellranger raw outputs
+
+assess_background: False
+downsample_background: True
+
+# -----------------------------------------------------
+# Files required for profiling ambient background or running dsb normalisation
+
+# The pipeline requires the raw_feature_bc_matrix folder from cellranger or equivalent,
+# specified in the submission file path with {mod}_filetype set to "cellranger," "cellranger_multi," or "10X_h5"
+# for automatic search of .h5 or matrix folder for profiling ambient background or running dsb normalization.
+
+#-------------------------------------------
+# Investigate per-channel antibody staining
+channel_col: sample_id
+save_norm_prot_mtx: False
+
+#----------------------
+# Protein normalization
+#----------------------
+
+normalisation_methods: clr
+
+#-----------------------------------------------
+# Centered log ratio (CLR) normalization options
+
+# margin determines whether you normalise per cell (as you would for RNA),
+# or by feature (recommended, due to the variable nature of prot assays).
+# CLR margin 1 is recommended for informative qc plots in this pipeline
+# 0 = normalise row-wise (per cell)
+# 1 = normalise column-wise (per feature, recommended)
+clr_margin: 1
+
+#--------------------------------------------------------------
+# Denoised and Scaled by Background (DSB) normalization options
+quantile_clipping: True