See What You Can Do with Genomic Analysis Plug-in:
About Genomic Analysis Plug-in:
Genomic Analysis Plug-in is a key extension for studies on chromosomal aberration, mRNA splicing, transcription factor network, epigenomics, which are using microarray or next generation sequencing (NGS) technologies. It also works to mediate multi-omics data for integrative analysis.
For example, the genomic location filter, which is one of tools included in this plug-in, extracts (or excludes) probes/tags which are located in up-/down-stream or overlapping regions of a particular set of genes. It's definitely useful when you want to know binding sites of a transcription factor within 2kb up-stream of up-regulated genes, when you want to search genes having highly DNA-methylated regions in their 1kb up-stream, and when you want to extract sequence tags covering only exonic regions. And more various tools for genomic-location-related analyses are included.
- Genomic Location Filter
- Extracting entries of the query track within up-/down-stream or overlapping regions of the reference track.
- Region Score Filter
- Filtering entries of Region by score.
- Measurement to Region
- Converting a Measurement List with processed signals or ch1 raw signals to a Region, which is independent from a Platform or Series.
- Create Intervals
- Jointing neighbors to smooth fluctuations and see the trends along chromosomes.
- Grouping entries within up-/down-stream or overlapping regions or bins to summarize.
- Find Region from Seq
- Searching locations of the query sequence against whole genome or specified regions.
- Get Sequence
- Extracting genome sequences of specified regions.
- Find Correlated Regions
- Finding entries having correlated (or anti-correlated) patterns over the experiment.
- Scatter Plot of Regions
- Drawing a scatter plot between two Regions.