| Biological samples |
|
| Human colonic epithelium, paired-end read files |
(Heiser et al., 2020) |
GEO: GSM4804820
|
| Human colonic epithelium, subsampled, paired-end read files |
(Heiser et al., 2020) |
GEO: GSM5068493
|
|
| Deposited data |
|
| Human reference genome assembly, release 85 |
(Yates et al., 2020) |
Ensembl ftp: ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
|
| Human reference gene annotation file, release 85 |
(Yates et al., 2020) |
Vanderbilt http: https://www.mc.vanderbilt.edu/vumcdept/cellbio/laulab/data/Homo_sapiens.GRCh38.85.annotated.gtf.gz
|
|
| Software and algorithms |
|
| Scanpy |
(Wolf et al., 2018) |
N/A |
| dropkick |
(Heiser et al., 2020) |
N/A |
| dropEst |
(Petukhov et al., 2018) |
N/A |
| scRNABatchQC |
(Liu et al., 2019) |
https://github.com/liuqivandy/ |
| STAR |
(Dobin et al., 2013) |
N/A |
| Go (1.15.6) |
N/A |
http://golang.org/ |
| Singularity (3.7.0) |
(Kurtzer et al., 2020) |
https://github.com/hpcng/singularity |
| GATK4 (4.1.9.0) |
(Van der Auwera et al., 2013) |
https://github.com/broadinstitute/gatk |
| STAR (2.7.6a) |
(Dobin et al., 2013) |
https://github.com/alexdobin/STAR |
| BamTools (>= 2.5.0) |
(Barnett et al., 2011) |
https://github.com/pezmaster31/bamtools |
| Boost (>= 1.54) |
(Schling, 2011) |
https://github.com/boostorg/boost |
| zlib (1.2.11) |
N/A |
https://github.com/madler/zlib |
| bzip2 (1.0.5) |
N/A |
https://gitlab.com/federicomenaquintero/bzip2 |
| CMake (>=3.0) |
N/A |
https://gitlab.kitware.com/cmake/cmake |
| gcc (>=4.8.5) |
N/A |
https://gcc.gnu.org/git/ |
| dropEst (0.8.6) |
(Petukhov et al., 2018) |
https://github.com/kharchenkolab/dropEst |
| Rcpp (1.0.5) |
(Eddelbuettel and Francois, 2011) |
https://github.com/RcppCore/Rcpp |
| R (>=3.5.0) |
(R Core Team (2020), 2020) |
https://www.r-project.org/ |
| RcppEigen (0.3.3.7.0) |
(Bates and Eddelbuettel, 2013) |
https://github.com/RcppCore/RcppEigen |
| RInside (0.2.16) |
(Bates and Eddelbuettel, 2013) |
https://github.com/eddelbuettel/rinside |
| Matrix (1.2-18) |
(R Core Team (2020), 2020) |
https://github.com/cran/Matrix |
| scRNABatchQC (0.10.3) |
(Liu et al., 2019) |
https://github.com/liuqivandy/scRNABatchQC |
| Python (>=3.8.0) |
(van Rossum and Drake, 2009) |
https://www.python.org/ |
| jupyterlab (2.3.0a1) |
(Kluyver et al., 2016) |
https://github.com/jupyterlab/jupyterlab |
| Jupyter (>=1.0.0) |
(Kluyver et al., 2016) |
https://github.com/jupyter |
| Scanpy (1.6.0) |
(Wolf et al., 2018) |
https://github.com/theislab/scanpy |
| AnnData (0.7.4) |
(Wolf et al., 2018) |
https://github.com/theislab/anndata |
| dropkick (1.2.1) |
(Heiser et al., 2020) |
https://github.com/Ken-Lau-Lab/dropkick |
| NetworkX (>=2.2) |
(Hagberg et al., 2008) |
https://github.com/networkx/networkx |
| python-igraph (>=0.7.1.post6) |
(Csardi and Nepusz, 2006) |
https://github.com/igraph/python-igraph |
| leidenalg (>=0.8.2) |
(Traag et al., 2019) |
https://github.com/vtraag/leidenalg |
| POT (>=0.6.0) |
(Flamary and Courty, 2017) |
https://github.com/PythonOT/POT |
| NumPy (>=1.17.4) |
(Harris et al., 2020) |
https://github.com/numpy/numpy |
| pandas (>=1.1.4) |
(Reback et al., 2020) |
https://github.com/pandas-dev/pandas |
| NVR |
Chen et al., 2018 |
https://github.com/Ken-Lau-Lab/NVR |
