Bulk RNA-seq
STAR aligner - this is commonly used to map the reads to the genome reference
The links below are for DESeq2, possibly the most commonly used R package for differential expression analysis:
Analyzing RNA-seq data with DESeq2
RNA-seq workflow: gene-level exploratory analysis and differential expression
Single cell RNA-seq
Current Best Practices in Single-Cell RNA-seq Analysis - a recently published tutorial
10x Genomics provides Cell Ranger software for 10x Chromium data processing and Loupe Cell Browser for data visualisation and simple analysis:
What is Cell Ranger? and Getting Started with Cell Ranger
What is Loupe Browser? and Loupe Browser Tutorial
Seurat package in R is commonly used for more sophisticated analysis and has many tutorials available. The tutorials below are particularly useful to start with:
Differential expression testing
Guided Clustering Tutorial