Software and Data

Software
  • SLIDE (Sparse Linear modeling of RNA-Seq data for Isoform Discovery and abundance Estimation)
    • Please cite the following paper in any research that uses this software package
      • Li, J.J., Jiang, C.-R., Brown, B.J., Huang, H., and Bickel, P.J. (2011). Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation. Proc Natl Acad Sci. USA 108(50):19867-19872.
    • (Updates on May 7th, 2012 -- A feature was added for estimating the annotated isoform abundance without doing isoform discovery.)
    • (Updates on Apr 18th, 2012 -- A feature was added for removing erroneously mapped reads; a bug of multiprocessing was fixed.)
    • (Updates on Apr 5th, 2012 -- A feature was added for handling single-end RNA-Seq reads or a mixture of single-end and paired-end reads.)
  • NMFP (Non-negative Matrix Factorization based Preselection)
    • Please cite the following paper in any research that uses this software package
      • Ye, Y. and Li, J.J. (2016). NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genomics in press.
  • TROM (TRanscriptome Overlap Measure)
Data
  • Estimates of D. melanogaster and C. elegans gene expression in different developmental stages, tissues and cells (in FPKM units)
    • D. melanogaster gene expression estimates in 30 fly developmental stages (download)
    • D. melanogaster gene expression estimates in 29 fly tissues and 19 fly cell lines (download)
    • C. elegans gene expression estimates in 35 worm developmental stages (download)
    • C. elegans gene expression estimates in 4 worm tissues and 14 worm dissected cells (download)
    • Please cite the following paper in any research that uses the above data
      • Li, J.J., Huang, H., Bickel, P.B., and Brenner, S.E. (2014). Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research 24(7):1086-1101.
    • For more details about the data, please refer to the section "Estimating gene expression in developmental stages and tissues/cells" in the Methods of the above paper ([html] [pdf]).
  • Associated promoter and enhancer regions identified based on signals of three histone modification marks (H3K4me1, H3K4me3 and H3K27ac) in 16 human tissue and cell types (download)