mtorresm55/longcell repository overview

Created from mtorresm55/longcellpre:v2.2 (might try clean from condaforge/miniforge3 if fails)

docker run -it c2366e22f0b9 /bin/bash

apt-get update

apt install build-essential

apt-get install libboost-dev

mamba install -c conda-forge -c bioconda -c r minimap2 samtools bedtools r-devtools bioconductor-iranges bioconductor-genomicranges r-rcppeigen bioconductor-rsamtools r-igraph r-rcppeigen bioconductor-bsgenome bioconductor-genomicfeatures r-parallelly r-listenv r-globals r-mass r-future r-data.table r-plyr r-proxy r-class r-future.apply r-nameneedle r-rcpphungarian r-transport r-e1071 r-reshape2 r-dbscan r-peakram r-spgs r-biocmanager bioconductor-bsgenome.mmusculus.ucsc.mm10 bioconductor-txdb.mmusculus.ucsc.mm10.knowngene r-nlme r-sitmo r-dqrng r-rcppprogress r-irlba r-rcppannoy r-fnn r-polyclip r-deldir r-spatstat.utils r-spatstat.data r-tensor r-abind r-goftest r-spatstat.sparse r-spatstat.random r-spatstat.geom r-colorspace r-viridislite r-rcolorBrewer r-munsell r-labeling r-farver r-scales r-mgcv r-isoband r-gtable r-rcpparmadillo r-gridextra r-ggplot2 r-kernsmooth r-catools r-gtools r-gplots r-here r-rcpptoml r-curl r-rmarkdown r-crosstalk r-lazyeval r-zoo r-reticulate r-survival r-dotcall64 r-spam r-progressr r-sp r-mvtnorm r-bdsmatrix r-numderiv r-uwot r-spatstat.explore r-sctransform r-scattermore r-rtsne r-rspectra r-rOcr r-rcpphnsw r-rann r-plotly r-pbapply r-patchwork r-lmtest r-leiden r-ica r-ggridges r-ggrepel r-fitdistrplus r-fastdummies r-cowplot r-cluster r-seuratobject r-bbmle r-latex2exp r-extradistr r-seurat

devtools::install_github("yuntianf/Longcell")