{"id":18,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/help-sheets\/"},"modified":"2022-11-04T13:50:22","modified_gmt":"2022-11-04T13:50:22","slug":"technical-help-sheets","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/technical-help-sheets\/","title":{"rendered":"Technical help sheets"},"content":{"rendered":"\n

Technical requirements for data analysis<\/h2>\n\n\n\n

You will require the following tools for executing the practicals in this course:<\/p>\n\n\n\n

Raw reads to Expression Matrix (EM)<\/h3>\n\n\n\n
CellRanger<\/td>https:\/\/support.10xgenomics.com\/single-cell-gene-expression\/software\/pipelines\/latest\/installation<\/a><\/td><\/tr>
SRA Toolkit<\/td>https:\/\/github.com\/ncbi\/sra-tools\/wiki\/02.-Installing-SRA-Toolkit<\/a><\/td><\/tr>
Fastqc<\/td>https:\/\/kb.10xgenomics.com\/hc\/en-us\/articles\/360048465032-When-to-run-FastQC-<\/a><\/td><\/tr>
TrimGalore<\/td>https:\/\/github.com\/FelixKrueger\/TrimGalore<\/a><\/td><\/tr>
R, dplyr<\/td>https:\/\/www.r-project.org\/nosvn\/pandoc\/dplyr.html<\/a><\/td><\/tr>
R, cowplot<\/td>https:\/\/cran.r-project.org\/web\/packages\/cowplot\/readme\/README.html<\/a><\/td><\/tr>
R, ggplot2<\/td>https:\/\/ggplot2.tidyverse.org\/<\/a><\/td><\/tr>
R, tibble<\/td>https:\/\/cran.r-project.org\/web\/packages\/tibble\/readme\/README.html<\/a><\/td><\/tr>
R, Matrix<\/td>https:\/\/rdrr.io\/rforge\/Matrix\/<\/a><\/td><\/tr>
R, readr<\/td>https:\/\/cran.r-project.org\/web\/packages\/readr\/readme\/README.html<\/a><\/td><\/tr>
R, pathwork<\/td>https:\/\/cran.r-project.org\/web\/packages\/patchwork\/readme\/README.html<\/a><\/td><\/tr>
R, tidyr<\/td>https:\/\/www.r-project.org\/nosvn\/pandoc\/tidyr.html<\/a><\/td><\/tr>
R, RColorBrewer<\/td>https:\/\/rdrr.io\/cran\/RColorBrewer\/<\/a><\/td><\/tr>
R, org.Hs.eg<\/a>.db<\/td>https:\/\/bioconductor.org\/packages\/release\/data\/annotation\/html\/org.Hs.eg.db.html<\/a><\/td><\/tr>
R, glmGamPoi<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/glmGamPoi.html<\/a><\/td><\/tr>
R, hdf5r<\/td>https:\/\/github.com\/hhoeflin\/hdf5r<\/a><\/td><\/tr>
R, DoubletFinder<\/td>https:\/\/github.com\/chris-mcginnis-ucsf\/DoubletFinder<\/a><\/td><\/tr>
Anaconda<\/td>https:\/\/www.anaconda.com\/products\/distribution#Downloads<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n


<\/p>\n\n\n\n

Pre-precessing and Dimensionality Reduction \/ From UMAP to Annotation<\/h3>\n\n\n\n
R Studio<\/td>https:\/\/www.rstudio.com\/products\/rstudio\/download\/<\/a><\/td><\/tr>
R, latest version<\/td>https:\/\/cran.r-project.org\/<\/a><\/td><\/tr>
Covid data, sample C143<\/td>https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSM4339771<\/a><\/td><\/tr>
Covid data, sample C145<\/td>https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSM4339773<\/a><\/td><\/tr>
Covid data, sample C51<\/td>https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSM4475048<\/a><\/td><\/tr>
Covid data, sample C52<\/td>https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSM4475049<\/a><\/td><\/tr>
R package SingleCellExperiment<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/SingleCellExperiment.html<\/a><\/td><\/tr>
R package Matrix<\/td>https:\/\/cran.r-project.org\/web\/packages\/Matrix\/index.html<\/a><\/td><\/tr>
R package DropletUtils<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/DropletUtils.html<\/a><\/td><\/tr>
R package scran<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/scran.html<\/a><\/td><\/tr>
R package batchelor<\/td>https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/batchelor.html<\/a><\/td><\/tr>
R package Seurat<\/td>https:\/\/cran.r-project.org\/web\/packages\/Seurat\/index.html<\/a><\/td><\/tr>
R package uwot<\/td>https:\/\/github.com\/jlmelville\/uwot<\/a><\/td><\/tr>
R package dplyr<\/td>https:\/\/cran.r-project.org\/web\/packages\/dplyr\/index.html<\/a><\/td><\/tr>
R package irlba<\/td>https:\/\/cran.r-project.org\/web\/packages\/irlba\/index.html<\/a><\/td><\/tr>
R package miloR (development version)<\/td>https:\/\/github.com\/MarioniLab\/miloR<\/a><\/td><\/tr>
R package stringr<\/td>https:\/\/cran.r-project.org\/web\/packages\/stringr\/index.html<\/a><\/td><\/tr>
R package gdata<\/td>https:\/\/cran.r-project.org\/web\/packages\/gdata\/index.html<\/a><\/td><\/tr>
R package DoubletFinder<\/td>https:\/\/github.com\/chris-mcginnis-ucsf\/DoubletFinder<\/a><\/td><\/tr>
R package ggplot2<\/td>https:\/\/ggplot2.tidyverse.org\/<\/a><\/td><\/tr>
R package ggpubr<\/td>https:\/\/cran.r-project.org\/web\/packages\/ggpubr\/index.html<\/a><\/td><\/tr>
R package MouseGastrulationData<\/td>https:\/\/bioconductor.org\/packages\/release\/data\/experiment\/html\/MouseGastrulationData.html<\/a><\/td><\/tr>
R package viridis<\/td>https:\/\/cran.r-project.org\/web\/packages\/viridis\/index.html<\/a><\/td><\/tr>
Magick++<\/td>https:\/\/imagemagick.org\/Magick++\/<\/a><\/td><\/tr>
R package igraph<\/td>https:\/\/cran.r-project.org\/web\/packages\/igraph\/index.html<\/a><\/td><\/tr>
R package celldex<\/td>http:\/\/bioconductor.org\/packages\/release\/data\/experiment\/html\/celldex.html<\/a><\/td><\/tr>
R package SingleR<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/SingleR.html<\/a><\/td><\/tr>
R package pheatmap<\/td>https:\/\/cran.r-project.org\/web\/packages\/pheatmap\/index.html<\/a><\/td><\/tr>
R package SC3<\/td>https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/SC3.html<\/a><\/td><\/tr>
R package Harmony<\/td>https:\/\/cran.r-project.org\/web\/packages\/harmony\/index.html<\/a><\/td><\/tr>
R package Seurat<\/td>https:\/\/cran.r-project.org\/web\/packages\/Seurat\/index.html<\/a><\/td><\/tr>
R package Azimuth<\/td>https:\/\/github.com\/satijalab\/azimuth<\/a><\/td><\/tr>
R package SeuratData<\/td>https:\/\/github.com\/satijalab\/seurat-data<\/a><\/td><\/tr>
R package patchwork<\/td>https:\/\/cran.r-project.org\/web\/packages\/patchwork\/index.html<\/a><\/td><\/tr>
R package bluster<\/td>https:\/\/bioconductor.org\/packages\/3.15\/bioc\/html\/bluster.html<\/a><\/td><\/tr>
R package scater<\/td>https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/scater.html<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n


<\/p>\n\n\n\n

Cell Atlases & Interpretation<\/h3>\n\n\n\n