category: Gene Expression

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
• dapple - Image Analysis for DNA Microarrays
• ExpressConverter - Convert microarray files to TIGR file formats
• 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
• magic - MicroArray Genome Imaging and Clustering Tool
• midas - Microarray Data Analysis System
• Rcorrector - Adjusts threshold for trusted kmers based on kmer frequency
• rnaspades - SPAdes Transcriptome Assembly
• SOAPdenovo-Trans - Transcriptome assembly
• stem - Short Time-series Expression Miner
• stringtie - assemble RNA-seq alignments into transcripts
• tmev - TIGR Multi-Experiment Viewer
• transrate - de-novo transcriptome assembly quality analysis
• Trinity - RNA-Seq De novo Assembly