Package
| Package Version
| License
| License Link
|
nextflow
| >=22.04.5, <=23.04.3
| Apache License 2.0
| https://github.com/nextflow-io/nextflow/blob/master/LICENSE
|
samtools
| 1.17
| MIT
| https://github.com/samtools/samtools/blob/develop/LICENSE
|
umi_tools
| 1.1.4
| MIT
| https://github.com/CGATOxford/UMI-tools/blob/master/LICENSE
|
star
| 2.6.1
| MIT
| https://github.com/alexdobin/STAR/blob/master/LICENSE
|
featureCount
| 2.0.1
| GPL-3
| https://bioconductor.org/packages/release/bioc/html/Rsubread.html
|
python
| 3.10.12
| PSF License
| https://docs.python.org/3/license.html
|
setuptools
| 70.1.1
| MIT
| https://github.com/pypa/setuptools/blob/main/LICENSE
|
compilers
| 1.6.0
| BSD 3-Clause
| https://github.com/conda-forge/compilers-feedstock/blob/main/LICENSE.txt
|
cython
| 3.0.5
| Apache-2.0
| https://github.com/cython/cython/blob/master/LICENSE.txt
|
click
| 8.1.7
| BSD-3-Clause
| https://github.com/pallets/click/blob/main/LICENSE.txt
|
rich-click
| 1.7.4
| MIT
| https://github.com/ewels/rich-click/blob/master/LICENSE
|
typer
| 0.12.3
| MIT
| https://github.com/fastapi/typer/blob/master/LICENSE
|
papermill
| 2.6.0
| BSD 3-Clause
| https://github.com/nteract/papermill/blob/main/LICENSE
|
pydantic
| 2.8.2
| MIT
| https://github.com/pydantic/pydantic/blob/main/LICENSE
|
pandas
| 2.1.3
| BSD 3-Clause
| https://github.com/pandas-dev/pandas/blob/main/LICENSE
|
numpy
| 1.26.2
| BSD 3-Clause
| https://github.com/numpy/numpy/blob/main/LICENSE.txt
|
pyarrow
| 12.0.1
| Apache License 2.0
| https://github.com/apache/arrow/blob/main/LICENSE.txt
|
biopython
| 1.81
| BSD 3-Clause
| https://github.com/biopython/biopython/blob/master/LICENSE.rst
|
pysam
| 0.21.0
| MIT
| https://github.com/pysam-developers/pysam/blob/master/COPYING
|
cytoolz
| 0.12.0
| BSD 3-Clause
| https://github.com/conda-forge/cytoolz-feedstock/blob/main/LICENSE.txt
|
python-Levenshtein
| 0.25.1
| GPL (>= 2)
| https://github.com/ztane/python-Levenshtein/blob/master/COPYING
|
colorlog
| 6.8.2
| MIT
| https://github.com/borntyping/python-colorlog/blob/master/LICENSE
|
humanize
| 4.10.0
| MIT
| https://github.com/python-humanize/humanize/blob/main/LICENCE
|
funcy
| 2
| BSD 3-Clause
| https://github.com/Suor/funcy/blob/master/LICENSE
|
scanpy
| 1.9.6
| BSD 3-Clause
| https://github.com/scverse/scanpy/blob/main/LICENSE
|
R
| 4.2.3
| GPL-2 and GPL-3
| https://cran.r-project.org/
|
stringi
| 1.8.3
| BSD-3-clause
| https://cran.r-project.org/package=stringi
|
tidyverse
| 1.3.2
| MIT
| https://cran.r-project.org/package=tidyverse
|
dplyr
| 1.1.4
| MIT
| https://cran.r-project.org/package=dplyr
|
ggplot2
| 3.5.0
| MIT
| https://cran.r-project.org/package=ggplot2
|
Seurat
| 4.1.1
| MIT
| https://cran.r-project.org/package=Seurat
|
arrow
| 12.0.1
| Apache License (>= 2.0)
| https://cran.r-project.org/package=arrow
|
viridis
| 0.6.5
| MIT
| https://cran.r-project.org/package=viridis
|
ggprism
| 1.0.5
| GPL (>= 3.0)
| https://cran.r-project.org/package=ggprism
|
knitr
| 1.46
| GPL
| https://cran.r-project.org/package=knitr
|
kableExtra
| 1.4.0
| MIT
| https://cran.r-project.org/package=kableExtra
|
RColorBrewer
| 1.1.3
| Apache License 2.0
| https://cran.r-project.org/package=RColorBrewer
|
fields
| 15.2
| GPL (>= 2)
| https://cran.r-project.org/package=fields
|
ggpubr
| 0.4.0
| GPL-2
| https://cran.r-project.org/package=ggpubr
|
cpp11
| 0.4.7
| MIT
| https://cran.r-project.org/package=cpp11
|
RcppZiggurat
| 0.1.6
| GPL (>= 2)
| https://cran.r-project.org/package=RcppZiggurat
|
RcppGSL
| 0.3.13
| GPL (>= 2)
| https://cran.r-project.org/package=RcppGSL
|
downloadthis
| 0.3.3
| MIT
| https://cran.r-project.org/package=downloadthis
|
Rfast2
| 0.1.3
| GPL (>= 2)
| https://cran.r-project.org/package=Rfast2
|
sceasy
| 0.0.7
| GPL-3
| https://github.com/cellgeni/sceasy/blob/master/LICENSE
|
anndata
| 0.7.5.4
| MIT
| https://cran.r-project.org/package=anndata
|
irlba
| 2.3.5.1
| GPL-3
| https://cran.r-project.org/package=irlba
|
Matrix
| 1.6.5
| GPL (>= 2)
| https://cran.r-project.org/package=Matrix
|
