Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

[1] Patel AP(2014)Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma Science 344 1396-401

[2] Tirosh I(2005)Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 15-20

[3] Trombetta JJ(2014)The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Nat Biotechnol 32 381-6

[4] Shalek AK(1996)R: a language for data analysis and graphics J Comput Graph Stat 5 299-314

[5] Gillespie SM(2007)Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 118-27

[6] Wakimoto H(2015)Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells Genome Biol 16 127-37

[7] Lewis BP(2016)Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma Genome Biol 17 80-2

[8] Burge CB(2007)Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS Genet 3 e161-40

[9] Bartel DP(2016)Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization PeerJ Prepr 4 e1839v1-50

[10] Trapnell C(1982)Least squares quantization in PCM IEEE Trans Inf Theory IEEE 28 129-605

[1] Patel AP(2014)Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma Science 344 1396-401

[2] Tirosh I(2005)Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 15-20

[3] Trombetta JJ(2014)The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Nat Biotechnol 32 381-6

[4] Shalek AK(1996)R: a language for data analysis and graphics J Comput Graph Stat 5 299-314

[5] Gillespie SM(2007)Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 118-27

[6] Wakimoto H(2015)Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells Genome Biol 16 127-37

[7] Lewis BP(2016)Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma Genome Biol 17 80-2

[8] Burge CB(2007)Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS Genet 3 e161-40

[9] Bartel DP(2016)Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization PeerJ Prepr 4 e1839v1-50

[10] Trapnell C(1982)Least squares quantization in PCM IEEE Trans Inf Theory IEEE 28 129-605