A wrapper script to automate quality and adapter trimming as well as quality control.
A simple way to perform quality control checks on raw sequence data coming from HTS pipelines.
Aggregate results from bioinformatics analyses across many samples into a single report.
A fast and sensitive alignment program for mapping HTS reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
A highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
For this analysis the following data was obtained from the Ensembl FTP (release 86) server:
Supplier of analytical instruments, lab equipment and specialty diagnostics. For this analysis, the following information was obtained from the product web page:
This community project provides tools for the analysis and comprehension of high-throughput genomic data.
Differential expression analysis of RNA-seq expression profiles with biological replication. Used here to import raw counts for all samples (including bulks, blanks, and single cells).
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.
Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.
The scde package implements a set of statistical methods for analysing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis.
This interactive website was created as an R Markdown Website
A network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R.
A plotting system for R, based on the grammar of graphics.
An integrated Bayesian hierarchical model where:
sessionInfo()## R Under development (unstable) (2017-11-09 r73698)
## Platform: x86_64-apple-darwin16.7.0 (64-bit)
## Running under: macOS High Sierra 10.13.3
##
## Matrix products: default
## BLAS: /usr/local/lib/R/lib/libRblas.dylib
## LAPACK: /usr/local/lib/R/lib/libRlapack.dylib
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] compiler_3.5.0 backports_1.1.2 magrittr_1.5 rprojroot_1.3-2
## [5] tools_3.5.0 htmltools_0.3.6 yaml_2.1.18 Rcpp_0.12.16
## [9] stringi_1.1.7 rmarkdown_1.9 knitr_1.20 stringr_1.3.0
## [13] digest_0.6.15 evaluate_0.10.1