diff --git a/README.html b/README.html new file mode 100644 index 0000000..ff66021 --- /dev/null +++ b/README.html @@ -0,0 +1,69 @@ + + rCASC + +Since the end of the 90’s omics high-throughput technologies have +generated an enormous amount of data, reaching today an exponential +growth phase. Analysis of omics big data is a revolutionary means of +understanding the molecular basis of disease regulation and +susceptibility, and this resource is accessible to the +biological/medical community via bioinformatics frameworks. However, +because of the fast evolution of computation tools and omics methods, +the /reproducibility crisis/ + is becoming a very +important issue [/Nature, 6 July 2018/ +] and there is a +mandatory need to to guarantee robust and reliable results to the +research community [/Global Engage Blog/ +]. + +Our group is deeply involved in developing workflows that guarantee both +*functional* (i.e. the information about data and the utilized tools are +saved in terms of meta-data) and *computation* reproducibility (i.e. the +real image of the computation environment used to generate the data is +stored). For this reason we have founded a bioinformatics community +called /reproducible-bioinformatics.org/ + /Kulkarni et al. BMC +Bioinformatics/ designed to provide to the +biological community a reproducible bioinformatics ecosystem [/Beccuti +et al. Bioinformatics 2018/ +]. + +rCASC, Cluster Analysis of Single Cells, is part of the +/reproducible-bioinformatics.org/ + project and provides +single cell analysis functionalities within the reproducible rules +described by Sandve et al. [/PLoS Comp Biol. 2013/ +]. +rCASC is designed to provide a complete workflow (Figure 1) for +cell-subpopulation discovery. + +Fig. 1:rCASC workflow + +Fig. 1:rCASC workflow + + + Installation + +|install.packages("devtools") +library(devtools) +install_github("kendomaniac/rCASC", ref="master")| + + + Requirements + +You need to have docker installed on your linux machine, for more info +see this document: https://docs.docker.com/engine/installation/. + +The functions in CASC package require that user is sudo or part of a +docker group. See the following document for more info: +https://docs.docker.com/engine/installation/linux/ubuntulinux/#/manage-docker-as-a-non-root-user + +IMPORTANT The first time casc is installed the downloadContainers needs +to be executed to download to the local repository the containers that +are needed for the use of docker4seq + +|library(rCASC) +downloadContainers()| + +More info: CASC vignette + diff --git a/man/SCannoByGtf.Rd b/man/SCannoByGtf.Rd index 2a8e3a2..c997622 100644 --- a/man/SCannoByGtf.Rd +++ b/man/SCannoByGtf.Rd @@ -43,7 +43,7 @@ This function executes the docker container annotate.1, where refGenome is used system("wget ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz") system("gunzip Mus_musculus.GRCm38.92.gtf.gz") scannobyGtf(group="docker", file=paste(getwd(),"lorenz_testSCumi_mm10.csv",sep="/"), - gtf.name="Mus_musculus.GRCm38.92.gtf", + gtf.name="Homo_sapiens.GRCh38.94.gtf", biotype="protein_coding", mt=TRUE, ribo.proteins=TRUE,umiXgene=3) }