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