Pinned Repositories
Annocript
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
Annocript_utils
A set of utilities to use with Annocript
bioperl-live
Core BioPerl 1.x code
DEA
Differential Expression analysis with Annocript (DEA) is a little package to make useful differential gene expression analyses and plots with GO and UniPathway enrichments.
gatk
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
HITI_OffTargetDetection
HMZDelFinder
CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data
hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
R-ecology
Data Carpentry R lessons on ecology
VarGenius
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!
frankMusacchia's Repositories
frankMusacchia/Annocript
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
frankMusacchia/VarGenius
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!
frankMusacchia/DEA
Differential Expression analysis with Annocript (DEA) is a little package to make useful differential gene expression analyses and plots with GO and UniPathway enrichments.
frankMusacchia/Annocript_utils
A set of utilities to use with Annocript
frankMusacchia/bioperl-live
Core BioPerl 1.x code
frankMusacchia/gatk
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
frankMusacchia/HITI_OffTargetDetection
frankMusacchia/HMZDelFinder
CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data
frankMusacchia/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
frankMusacchia/R-ecology
Data Carpentry R lessons on ecology
frankMusacchia/UsefulScripts
Useful scripts for anything I do in Bioinformatics
frankMusacchia/VarGenius-HZD
A sensitive tool to call rare homozygous deletions from a dataset of BAM files