# HG changeset patch # User jjohnson # Date 1386947536 18000 # Node ID bb5e68f15713fe9f6d0031cd13a8ff4e7994b462 Uploaded diff -r 000000000000 -r bb5e68f15713 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Dec 13 10:12:16 2013 -0500 @@ -0,0 +1,164 @@ + + + + + + + + + http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.8.tar.gz + make + $INSTALL_DIR/bin/sam + + sam/samtools + $INSTALL_DIR/bin/sam + + + convert-sam-for-rsem + $INSTALL_DIR/bin + + + extract-transcript-to-gene-map-from-trinity + $INSTALL_DIR/bin + + + rsem-bam2readdepth + $INSTALL_DIR/bin + + + rsem-bam2wig + $INSTALL_DIR/bin + + + rsem-build-read-index + $INSTALL_DIR/bin + + + rsem-calculate-credibility-intervals + $INSTALL_DIR/bin + + + rsem-calculate-expression + $INSTALL_DIR/bin + + + rsem-extract-reference-transcripts + $INSTALL_DIR/bin + + + rsem-gen-transcript-plots + $INSTALL_DIR/bin + + + rsem-get-unique + $INSTALL_DIR/bin + + + rsem-parse-alignments + $INSTALL_DIR/bin + + + rsem-plot-model + $INSTALL_DIR/bin + + + rsem-plot-transcript-wiggles + $INSTALL_DIR/bin + + + rsem-prepare-reference + $INSTALL_DIR/bin + + + rsem-preref + $INSTALL_DIR/bin + + + rsem-run-em + $INSTALL_DIR/bin + + + rsem-run-gibbs + $INSTALL_DIR/bin + + + rsem-simulate-reads + $INSTALL_DIR/bin + + + rsem-synthesis-reference-transcripts + $INSTALL_DIR/bin + + + rsem-tbam2gbam + $INSTALL_DIR/bin + + + rsem-control-fdr + $INSTALL_DIR/bin + + + rsem-generate-data-matrix + $INSTALL_DIR/bin + + + rsem-generate-ngvector + $INSTALL_DIR/bin + + + rsem-run-ebseq + $INSTALL_DIR/bin + + + rsem-sam-validator + $INSTALL_DIR/bin + + + rsem-scan-for-paired-end-reads + $INSTALL_DIR/bin + + + rsem_perl_utils.pm + $INSTALL_DIR/bin + + + + + + + make ebseq + $INSTALL_DIR/bin/EBSeq + + EBSeq/EBSeq + $INSTALL_DIR/bin/EBSeq + + + EBSeq/blockmodeling + $INSTALL_DIR/bin/EBSeq + + + EBSeq/rsem-for-ebseq-find-DE + $INSTALL_DIR/bin/EBSeq + + + EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info + $INSTALL_DIR/bin/EBSeq + + + $INSTALL_DIR/bin + + + + +RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly +interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, +variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels. +For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files +can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV). +Transcript-coordinate files can be visualized by IGV. + +http://deweylab.biostat.wisc.edu/rsem/README.html +http://deweylab.biostat.wisc.edu/rsem/ + + +