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github.com/10XGenomics/cellranger @cellranger-10.0.0

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7,670 symbols 24,454 edges 795 files 2,615 documented · 34%

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README

Cell Ranger is a set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from 10x Genomics Chromium Single Cell data.

Please note that this source code is made available only for informational purposes. 10x does not provide support for interpreting, modifying, building, or running this code.

The officially supported release binaries are available at https://www.10xgenomics.com/support/software/cell-ranger/downloads. Documentation is available at https://www.10xgenomics.com/support/software/cell-ranger.

Extension points exported contracts — how you extend this code

AsMetricPrefix (Interface)

The string used in a metric name. [10 implementers]

lib/rust/metric/src/lib.rs

Bucketizer (Interface)

Converts a raw metric to a bucketed value. [6 implementers]

lib/go/telemetry/config/compile.go

AlertElementProps (Interface)

(no doc)

lib/typescript/websummary/src/components/OptionalMultiplexedSummary/AlertElement.tsx

Metric (Interface)

The core trait in this crate. Any data structure representing a metric will implement this trait. It may be auto derived [9 …

lib/rust/metric/src/lib.rs

ValueContext (Interface)

This allows e.g. command line flags to be passed in to the value extractor. [1 implementers]

lib/go/telemetry/collector/value.go

HeaderWithHelpProps (Interface)

(no doc)

lib/typescript/websummary/src/components/OptionalMultiplexedSummary/TitledComponents.tsx

JsonReport (Interface)

`JsonReport` trait defines how a structure would be written out to a metric summary json file. It has a single function [17 …

lib/rust/metric/src/lib.rs

ValueExtractor (Interface)

A source of metric data. This gets a little bit complicated because of performance requirements. We need to be able to [1 …

lib/go/telemetry/collector/value.go

Core symbols most depended-on inside this repo

map

called by 1339

lib/rust/barcode/src/lib.rs

collect

called by 760

lib/rust/cr_wrap/src/telemetry.rs

push

called by 742

lib/rust/fastq_set/src/array.rs

len

called by 599

lib/rust/vdj_asm_utils/src/graph_read.rs

len

called by 587

lib/rust/vdj_proto/src/io.rs

iter

called by 462

lib/rust/cr_types/src/spill_vec.rs

into_iter

called by 301

lib/rust/metric/src/lib.rs

iter

called by 296

lib/rust/metric/src/lib.rs

Shape

Function 3,255

Method 2,919

Class 1,212

Enum 138

Struct 70

Interface 66

TypeAlias 9

FuncType 1

Languages

Rust62%

Python29%

Go6%

TypeScript3%

C1%

Modules by API surface

lib/rust/multi/src/config/mod.rs175 symbols

lib/python/cellranger/matrix.py137 symbols

lib/rust/cr_types/src/probe_set.rs102 symbols

lib/rust/cr_lib/src/stages/detect_chemistry.rs97 symbols

lib/rust/cr_types/src/types.rs95 symbols

lib/python/cellranger/molecule_counter.py88 symbols

lib/rust/cr_types/src/rna_read.rs87 symbols

lib/rust/cr_types/src/chemistry/mod.rs85 symbols

lib/python/cellranger/vdj/annotations.py82 symbols

lib/rust/cr_aggr/src/parse_aggr_csv.rs79 symbols

lib/rust/vdj_ann/src/annotate.rs76 symbols

lib/rust/barcode/src/lib.rs73 symbols

For agents

$ claude mcp add cellranger \
  -- python -m otcore.mcp_server <graph>

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github.com/10XGenomics/cellranger @cellranger-10.0.0

Extension points exported contracts — how you extend this code

Core symbols most depended-on inside this repo

Shape

Languages

Modules by API surface

For agents

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