Chimeric antigen receptor (CAR) T-cell therapy has produced remarkable anti-tumor responses in patients with B-cell malignancies. However, clonal kinetics and transcriptional programs that regulate the fate of CAR-T cells after infusion remain poorly understood.<br>
Single-cell RNA sequencing (scRNA-seq) was performed to profile CD8+ CAR-T cells from infusion products (IPs) and blood of patients undergoing CD19 CAR-T immunotherapy.
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Original publication is available <a href="https://pubmed.ncbi.nlm.nih.gov/31924795/", target="_blank">here</a>.

Comprehensive analysis of transcriptome data

This package translates microarray expression data into metadata
  of reduced dimension. It provides various sample-centered and group-centered
  visualizations, sample similarity analyses and functional enrichment analyses.
  The underlying SOM algorithm combines feature clustering, multidimensional
  scaling and dimension reduction, along with strong visualization capabilities.
  It enables extraction and description of functional expression modules inherent
  in the data.

fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods

Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>, Hoang Thanh Le <le@izbi.uni-leipzig.de> and Martin Kalcher <mkalcher@porkbox.net>

GeneExpression, DifferentialExpression, GeneSetEnrichment,
DataRepresentation, Visualization

Routines for simple graphs and network analysis. It can
  handle large graphs very well and provides functions for generating random
  and regular graphs, graph visualization, centrality methods and much more.

graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0),
stats, utils

ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk,
testthat

gmp (optional), libxml2 (optional), glpk (optional)

'adjacency.R' 'auto.R' 'assortativity.R' 'attributes.R'
'basic.R' 'bipartite.R' 'centrality.R' 'centralization.R'
'cliques.R' 'cocitation.R' 'cohesive.blocks.R' 'community.R'
'components.R' 'console.R' 'conversion.R' 'data_frame.R'
'decomposition.R' 'degseq.R' 'demo.R' 'embedding.R' 'epi.R'
'fit.R' 'flow.R' 'foreign.R' 'games.R' 'glet.R' 'hrg.R'
'igraph-package.R' 'incidence.R' 'indexing.R' 'interface.R'
'iterators.R' 'layout.R' 'layout_drl.R' 'lazyeval.R' 'make.R'
'minimum.spanning.tree.R' 'motifs.R' 'nexus.R' 'operators.R'
'other.R' 'package.R' 'palette.R' 'par.R' 'paths.R' 'plot.R'
'plot.common.R' 'plot.shapes.R' 'pp.R' 'print.R' 'printr.R'
'random_walk.R' 'rewire.R' 'scan.R' 'scg.R' 'sgm.R'
'similarity.R' 'simple.R' 'sir.R' 'socnet.R' 'sparsedf.R'
'structural.properties.R' 'structure.info.R' 'test.R'
'tkplot.R' 'topology.R' 'triangles.R' 'utils.R' 'uuid.R'
'versions.R' 'weakref.R' 'zzz-deprecate.R'