Hi All,
I haven't posted anything here on FindPeaks since the early alpha testing days, so I thought I'd give a quick update.
First of all, the application is now in a "final" stage, as FindPeaks 3.1.9.2. It can be downloaded here. It comes with manuals and several useful tools for dealing with Short reads, and creating UCSC viewable tracks for genomic data.
Additionally, it has now been published as a bioinformatics application note (here) The article is open access, so no subscription is required to see it.
There are several things in the works as well. Features currently in development include: Paired End Tag-ChIP-Seq analysis, processing several new types of aligner data (MAQ .map files, SOAP, etc.), and an improved False Discovery Rate technique.
Finally, the next version of FindPeaks will also be released as an open source package (tentatively named the Vancouver Short Read Analysis Package) through Sourceforge. The package will also include several other programs that use the same infrastructure for SNP detection, non-synonymous SNP detection, exon/transcript/gene coverage and alternative splicing information, etc. I'll post the link to the full source, once it's available.
While I also watch this forum and take part in discussions here, I've also set up a mailing list for the FindPeaks application through Sourceforge. If you have any questions about the application, you can continue to email me, or you can now also write to the community of users. (Subscribe here.)
Happy ChIP-Seq-ing. (=
Anthony
I haven't posted anything here on FindPeaks since the early alpha testing days, so I thought I'd give a quick update.
First of all, the application is now in a "final" stage, as FindPeaks 3.1.9.2. It can be downloaded here. It comes with manuals and several useful tools for dealing with Short reads, and creating UCSC viewable tracks for genomic data.
Additionally, it has now been published as a bioinformatics application note (here) The article is open access, so no subscription is required to see it.
There are several things in the works as well. Features currently in development include: Paired End Tag-ChIP-Seq analysis, processing several new types of aligner data (MAQ .map files, SOAP, etc.), and an improved False Discovery Rate technique.
Finally, the next version of FindPeaks will also be released as an open source package (tentatively named the Vancouver Short Read Analysis Package) through Sourceforge. The package will also include several other programs that use the same infrastructure for SNP detection, non-synonymous SNP detection, exon/transcript/gene coverage and alternative splicing information, etc. I'll post the link to the full source, once it's available.
While I also watch this forum and take part in discussions here, I've also set up a mailing list for the FindPeaks application through Sourceforge. If you have any questions about the application, you can continue to email me, or you can now also write to the community of users. (Subscribe here.)
Happy ChIP-Seq-ing. (=
Anthony
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