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Releases: Fu-Yilei/SniffCell
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SniffCell v0.9.8a1
5hmC-aware SniffCell alpha
This prerelease adds separate 5mC and 5hmC marker discovery and read scoring,
while retaining the original modifiedC atlas path. It is published from
5hmC_compatitible_atlas for early testing.
Read the benchmark blog and detailed implementation update
for bar plots, control definitions, and the compatibility checks.
Install
pip install 'sniffcell==0.9.8a1'
sniffcell --versionThe package version is 0.9.8a1; the Git tag is v0.9.8a1. This is an alpha,
not a stable release. Normal stable installs remain on v0.9.7. The container
is published under ghcr.io/fu-yilei/sniffcell:0.9.8a1 when its build finishes;
this prerelease does not move Docker latest.
Atlas and input behavior
Download the four-donor GRCh38 brain atlas:
489,972 scoring rows, including the original 152,961-row paper backbone,
194,662 added 5mC markers, and 142,349 added 5hmC markers. The atlas is a
separate download, not bundled in the Python wheel.
With --bam-modification auto, each marker uses its declared channel.
Separate m/h BAM calls supply both assays. With an m-only BAM, h-specific
markers have no evidence; missing h is not treated as measured zero 5hmC.
An m tag alone does not distinguish a pure-5mC model from an older
modifiedC-like model. Existing unlabeled catalogs retain modifiedC behavior.
MDB-based discovery additionally needs the MDB dependency and source inputs;
using the precomputed catalog for deconvolution does not require rebuilding MDB.
Held-out evidence
On the same 46,373,872 bcontrol1 FANS control reads:
| Atlas | Precision | Recall | Correct assignments |
|---|---|---|---|
| Original paper backbone | 87.01% | 18.33% | 8,502,346 |
| Integrated dual | 88.64% | 31.03% | 14,391,267 |
The benchmark atlas excludes bcontrol1 from ONT discovery and reference means.
The distributed atlas includes all four donors and is a distinct artifact.
These results are a single-donor proof, not an independent validation of the
four-donor build or an estimate of the contribution of 5hmC alone. Other folds,
bulk checks, and single-channel ablations remain deferred.
Validation and compatibility
The main-branch tissue atlases, CLI update, and packaging changes are merged.
The merged source passed 273 tests plus 3 subtests. FGF14 historical-code
compatibility passed, and the post-merge backbone and dual runs reproduced
all eight benchmark output tables exactly. Genome-wide old-code parity has
not been established. The original paper backbone fields in the distributed
catalog are preserved exactly.
Full Changelog: v0.9.7...v0.9.8a1
SniffCell v0.9.7
Contributors
Assets 4
SniffCell Lite v0.9.6
Full Changelog: v0.9.5...v0.9.6
SniffCell v0.9.4
Full Changelog: v0.9.3...v0.9.4
SniffCell v0.9.3
Full Changelog: v0.9.2...v0.9.3
SniffCell v0.9.2
What's Changed
Full Changelog: v0.9.1...v0.9.2
Contributors
Assets 4
SniffCell v0.9.1
Full Changelog: v0.9.0...v0.9.1
SniffCell v0.9.0
Full Changelog: v0.8.0...v0.9.0
SniffCell v0.8.0
Full Changelog: v0.7.0...v0.8.0
SniffCell v0.7.0
Added Deconv function, where SniffCell can split the BAM into 2 Groups.