Commit 2dd45245 authored by Ruqian Lyu's avatar Ruqian Lyu
Browse files

docker file update

parent a898f0b1
......@@ -170,17 +170,19 @@ RUN sudo apt-get install -yq --no-install-recommends libudunits2-0 libudunits2-d
RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/leidenbase"))'
RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/monocle3"))'
RUN Rscript -e 'devtools::install_github(c("ChristophH/sctransform"))'
# install github packages
RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs"))'
RUN Rscript -e 'install.packages(c("foreach"))'
RUN Rscript -e 'install.packages(c("iterators"))'
RUN Rscript -e 'install.packages(c("rsample"))'
RUN Rscript -e 'install.packages(c("Rcpp"))'
RUN Rscript -e 'install.packages(c("rstan"))'
RUN Rscript -e 'install.packages(c("gam"))'
RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/monocle3"))'
RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs"))'
# install github packages
RUN Rscript -e 'devtools::install_github(c("Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"))'
......@@ -191,6 +193,19 @@ COPY ./ /home/jovyan
# add course files
COPY course_files /home/jovyan
COPY case_study_data/case_study.Rmd /home/jovyan/
COPY case_study_data/pre_processing_fq.Rmd /home/jovyan/
COPY mig-sc-workshop-2019-data.tar.gz /home/jovyan/data/
# cp data/droplet_id_example_per_barcode.txt.gz /home/jovyan/data/ && \
# cp data/pancreas -r /home/jovyan/data/ && \
# cp data/tung -r /home/jovyan/data/ && \
# cp data/2000_reference.transcripts.fa /home/jovyan/data/ && \
# cp data/droplet_id_example_truth.gz /home/jovyan/data/ && \
# cp data/deng -r /home/jovyan/data/ && \
# cp data/EXAMPLE.cram /home/jovyan/data/ && \
# cp data/sce -r /home/jovyan/data/
RUN chmod -R 777 /home/jovyan
......@@ -1127,3 +1127,43 @@ doi = {10.18637/jss.v059.i10}
language = "en",
doi = "10.1101/574574"
title = "scds: Computational Annotation of Doublets in {Single-Cell} {RNA}
Sequencing Data",
author = "Bais, Abha S and Kostka, Dennis",
abstract = "MOTIVATION: Single-cell RNA sequencing (scRNA-seq) technologies
enable the study of transcriptional heterogeneity at the
resolution of individual cells and have an increasing impact on
biomedical research. However, it is known that these methods
sometimes wrongly consider two or more cells as single cells, and
that a number of so-called doublets is present in the output of
such experiments. Treating doublets as single cells in downstream
analyses can severely bias a study's conclusions, and therefore
computational strategies for the identification of doublets are
needed. RESULTS: With scds, we propose two new approaches for in
silico doublet identification: Co-expression based doublet
scoring (cxds) and binary classification based doublet scoring
(bcds). The co-expression based approach, cxds, utilizes
binarized (absence/presence) gene expression data and, employing
a binomial model for the co-expression of pairs of genes, yields
interpretable doublet annotations. bcds, on the other hand, uses
a binary classification approach to discriminate artificial
doublets from original data. We apply our methods and existing
computational doublet identification approaches to four data sets
with experimental doublet annotations and find that our methods
perform at least as well as the state of the art, at comparably
little computational cost. We observe appreciable differences
between methods and across data sets and that no approach
dominates all others. In summary, scds presents a scalable,
competitive approach that allows for doublet annotation of data
sets with thousands of cells in a matter of seconds.
AVAILABILITY: scds is implemented as a Bioconductor R package
(doi: 10.18129/B9.bioc.scds). SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online.",
journal = "Bioinformatics",
month = sep,
year = 2019,
language = "en"
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