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Name: Francesco
Type: User
Company: Italian Institue of Technology
Location: Naples
Name: Francesco
Type: User
Company: Italian Institue of Technology
Location: Naples
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript
A set of utilities to use with Annocript
Core BioPerl 1.x code
Differential Expression analysis with Annocript (DEA) is a little package to make useful differential gene expression analyses and plots with GO and UniPathway enrichments.
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data
Specifications of SAM/BAM and related high-throughput sequencing file formats
Data Carpentry R lessons on ecology
Useful scripts for anything I do in Bioinformatics
VarGenius is a software for variants discovery and annotation. It allows efficient management of folder data and jobs submission into a PBS cluster. All the variants will be inserted into a PostgreSQL database that can be used for downstream analyses. It is written with PERL, R and HTML languages and uses Picard, Samtools, BWA, GATK and Annovar!
A sensitive tool to call rare homozygous deletions from a dataset of BAM files
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