encodeCells


This data includes RNA-seq quantifications for 56668 genes
in 2 cell lines with 2 replicates (GM12878 and K562), by
9 methods including RSEM, Cufflinks, FluxCapacitor, eXpress
and Sailfish etc. Gene meta information is included such as
gene name, gene type and if house keeping genes. Also, fold
changes for part of protein coding genes from microarray is
provided between these cell lines.


Several quantitative and visualized benchmarks
for RNA-seq quantification pipelines. Two-replicate
quantifications for genes, transcripts, junctions or
exons by each pipeline with nessasery meta information
should be organizd into numeric matrix in order to
proceed the evaluation.

Mingxiang Teng

rnaseqcomp

Benchmark for RNA-seq Quantification Pipelines

encodeCells function

A list of objects including two 56668*18
quantification matrices (gm12878 & k562), one 56668*3
dataframe of gene meta information (genemeta), one factor
documenting pipelines of RNA-seq replicates (repInfo) and
fold change from microarray (arrayFC).

encodeCells: Two Cell Lines from ENCODE by 9 Methods

Description

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