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
    • Important note: SLIDE is compatible with RNA-seq .bam files mapped by TopHat and TopHat2.
    • (Updates on Jan 30th, 2018 -- Several bugs have been fixed for RNA-seq .bam files with more than one read lengths.)
    • (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.)

 

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)