@@ 1967,6 1967,53 @@ cell types. Cell2cell is suitable for single-cell RNA sequencing
from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
(license license:bsd-3)))
+(define-public python-celltypist
+ (package
+ (name "python-celltypist")
+ (version "1.6.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Teichlab/celltypist")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0c42cx01zkxr0dk5f1d7q71qdi18v2smlc3wpvwyjlzplya7k2iy"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ '(modify-phases %standard-phases
+ (add-before 'check 'set-home
+ ;; The sanity check requires a HOME directory, because celltypist
+ ;; wants to write settings.
+ (lambda _ (setenv "HOME" "/tmp")))
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'build 'set-numba-cache-dir
+ (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (propagated-inputs
+ (list python-click
+ python-leidenalg
+ python-numpy
+ python-openpyxl
+ python-pandas
+ python-scanpy
+ python-scikit-learn
+ python-requests))
+ (home-page "https://github.com/Teichlab/celltypist")
+ (synopsis "Tool for semi-automatic cell type classification")
+ (description
+ "CellTypist is an automated cell type annotation tool for scRNA-seq
+datasets on the basis of logistic regression classifiers optimised by the
+stochastic gradient descent algorithm. CellTypist allows for cell prediction
+using either built-in (with a current focus on immune sub-populations) or
+custom models, in order to assist in the accurate classification of different
+cell types and subtypes.")
+ (license license:expat)))
+
(define-public python-cmseq
(package
(name "python-cmseq")