Package: CCB

CCB - Johns Hopkins Center for Computational Biology
Documentation
Web site	http://www.ccb.jhu.edu/software.shtml
Data
Platforms: linux-x86_64, osx-x86_64
Installation: BIRCH
Programs:
cuffcompare - compare the transcriptomes assembled from different RNA-Seq libraries cuffdiff - Compare expression levels of genes and transcripts in RNA-Seq experiments cufflinks - assembles transcriptomes from RNA-Seq data and quantifies their expression cuffmerge - merge transcriptome assemblies into a master transcriptome cuffnorm - normalize the expression levels from a set of RNA-Seq libraries cuffquant - Quantify gene and transcript expression in RNA-Seq samples gffcompare - compare, merge, annotate and estimate accuracy of one or more GFF files gffread - Filters and/or converts GFF3/GTF2 records gtf_2_sam - convert gtf files to sam files hisat2 - Align RNAseq reads to a hisat2-indexed genome hisat2-build - Build an index of a genome for use by hisat2 hisat2-inspect - print FASTA records from a hisat2 index in fields specified by options stringtie - assemble RNA-seq alignments into transcripts