HOMER

csRNA-seq: Technique that isolates 5' capped, short RNAs (20-60nt) from total RNA to map initiating transcripts genome-wide. Maps transcription activity at regulatory elements and efficiently captures initiation from both promoters and enhancer regions. (also works for Start-seq/5'GRO-seq/GRO-cap/PRO-cap/TSS-seq/5'RNA-seq, etc.)

ChIP-Seq: (Tutorials 1-10 above are geared toward ChIP-Seq and RNA-Seq) Isolation and sequencing of genomic DNA "bound" by a specific transcription factor, covalently modified histone, or other nuclear protein.  This methodology provides genome-wide maps of factor binding.  Most of HOMER's routines cater to the analysis of ChIP-Seq data.

RNA-Seq: (This one is currently only a quick-recipe driven list of commands, but the tutorials 1-3, & 8 above are geared toward RNA-Seq) Extraction, fragmentation, and sequencing of RNA. There are many variants on RNA-seq too, such as Ribo-Seq (isolation of ribosomes translating RNA), small RNA-Seq (to identify miRNAs), etc.

GRO-Seq: RNA-Seq of nascent RNA.  Transcription is halted, nuclei are isolated, labeled nucleotides are added back, and transcription briefly restarted resulting in labeled RNA molecules.  These newly created, nascent RNAs are isolated and sequenced to reveal "rates of transcription" as opposed to the total number of stable transcripts measured by normal RNA-seq.

Hi-C: Genomic interaction assay for understanding genome 3D structure.  This assay is much more specialized - For more information about how to use HOMER to analyze Hi-C data, check out the Hi-C analysis section.

DNase-Seq: Treatment of nuclei with a restriction enzyme such as DNase I will result in cleavage of DNA at accessible regions.  Isolation of these regions and their detection by sequencing allows the creation of DNase hypersensitivity maps, providing information about which regulatory elements are accessible in the genome.