diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 174 |
1 files changed, 173 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22b70a136f..a74002334b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -806,6 +806,44 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public python-cellbender + (package + (name "python-cellbender") + (version "0.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/CellBender") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3")))) + (build-system python-build-system) + (arguments + (list #:tests? #false)) ;there are none + (propagated-inputs + (list python-anndata + python-matplotlib + python-numpy + python-pandas + python-pyro-ppl + python-scikit-learn + python-scipy + python-sphinx + python-sphinx-argparse + python-sphinx-autodoc-typehints + python-sphinx-rtd-theme + python-sphinxcontrib-programoutput + python-tables)) + (home-page "https://cellbender.rtfd.io/") + (synopsis "Eliminate technical artifacts from single-cell RNA-seq data") + (description + "CellBender is a software package for eliminating technical artifacts +from high-throughput single-cell RNA sequencing (scRNA-seq) data.") + (license license:bsd-3))) + (define-public python-htsget (package (name "python-htsget") @@ -7167,6 +7205,64 @@ sequence.") auROC analysis.") (license license:gpl3)))) +(define-public r-sccustomize + (let ((commit "8414d1f5fb32277855b0619191a568932b7baeb0") + (revision "1")) + (package + (name "r-sccustomize") + (version (git-version "0.7.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samuel-marsh/scCustomize") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wcgfq7lx83a2kf8pjbw524gdvxf351n08cwd5wzmmy57kf4knbj")))) + (properties `((upstream-name . "scCustomize"))) + (build-system r-build-system) + (propagated-inputs + (list r-circlize + r-colorway + r-cowplot + r-data-table + r-dittoseq + r-dplyr + r-forcats + r-ggbeeswarm + r-ggplot2 + r-ggprism + r-ggpubr + r-ggrastr + r-ggrepel + r-glue + r-janitor + r-magrittr + r-matrix + r-paletteer + r-patchwork + r-pbapply + r-purrr + r-remotes + r-scales + r-scattermore + r-seurat + r-seuratobject + r-stringi + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/samuel-marsh/scCustomize") + (synopsis "Custom visualization and analyses of single-cell sequencing") + (description + "This is a collection of functions created and/or curated to aid in the +visualization and analysis of single-cell data using R.") + (license license:gpl3+)))) + (define-public r-snapatac (package (name "r-snapatac") @@ -13520,6 +13616,53 @@ transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.") (license license:gpl3+))) +(define-public python-ikarus + (package + (name "python-ikarus") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ikarus" version)) + (sha256 + (base32 + "086czpvj4yafz4vrq5rx2gy0bj2l8nzwnkk0gw8qvy4w133xjysy")))) + (build-system python-build-system) + (arguments + `(#:tests? #false + #:phases + (modify-phases %standard-phases + ;; See https://github.com/BIMSBbioinfo/ikarus/issues/12 + (add-after 'unpack 'fix-issue-12 + (lambda _ + (substitute* "ikarus/classifier.py" + (("pyscenic.genesig") "ctxcore.genesig")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs + (list python-numpy + python-pandas + python-scipy + python-scanpy + python-anndata + python-ctxcore ;because of issue 12 + pyscenic)) + (home-page "https://github.com/BIMSBbioinfo/ikarus") + (synopsis "Machine learning classifier of tumor cells") + (description + "ikarus is a stepwise machine learning pipeline that tries to cope with a task +of distinguishing tumor cells from normal cells. Leveraging multiple +annotated single cell datasets it can be used to define a gene set specific to +tumor cells. First, the latter gene set is used to rank cells and then to +train a logistic classifier for the robust classification of tumor and normal +cells. Finally, sensitivity is increased by propagating the cell labels based +on a custom cell-cell network. ikarus is tested on multiple single cell +datasets to ascertain that it achieves high sensitivity and specificity in +multiple experimental contexts.") + (license license:expat))) + (define-public vbz-compression (package (name "vbz-compression") @@ -14459,7 +14602,7 @@ The output is in SAM format.") (propagated-inputs (list libxml2)) (native-inputs - (list check-0.14 swig)) + (list check swig)) (home-page "http://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") (description "LibSBML is a library to help you read, write, manipulate, @@ -15734,6 +15877,35 @@ workflows from concise descriptions in ccwl. It is implemented as an language.") (license license:gpl3+))) +(define-public hh-suite + (package + (name "hh-suite") + (version "3.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/soedinglab/hh-suite") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bcmzg0ii6nkda2xm5jdddbwkgsag7k38j20af0c9chr2mbxwx4d")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "lib/simde")))) + (build-system cmake-build-system) + (arguments '(#:tests? #false)) ;no test target + (inputs + (list openmpi simde)) + (native-inputs + (list perl pkg-config xxd)) + (home-page "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7") + (synopsis "Remote protein homology detection suite") + (description "The HH-suite is a software package for sensitive protein sequence searching +based on the pairwise alignment of hidden Markov models (HMMs).") + (license license:gpl3+))) + (define-public wfmash (package (name "wfmash") |