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Table 2 Tools for investigating heterogeneity

From: Using single-cell multiple omics approaches to resolve tumor heterogeneity

Name

Description

Link

Input

Specific to single-cell

References

Accessibility

Databases

 scRNASeqDB

A database for gene expression profiling in human single cell by RNA-seq

https://bioinfo.uth.edu/scrnaseqdb/

N/A

Yes

Cao et al. [62]

***

 The Human Protein Atlas

Spatial distribution of protein expressions

http://www.proteinatlas.org/

Protein name

No

Uhlén et al. [108, 109]  

*****

 Enrichr

Very complete meta-database

http://amp.pharm.mssm.edu/Enrichr/enrich

List of genes/proteins—BED file

No

Kuleshov et al. [110]

*****

 CIViC

Clinical interpretation of cancer variant

https://civic.genome.wustl.edu/home

Gene or variant ID

No

Griffith et al. [111]

****

 MyGene2

A portal for sharing health and genetic information

https://www.mygene2.org

Genetic information

No

Xin et al. [112]

****

Genome sequencing

 SCITE

Pseudo-temporal clonal tree construction

https://github.com/cbg-ethz/SCITE

Presence/absence/unknown mutation matrix

Yes

Jhan et al. [113]

*

 oncoNEM

Pseudo-temporal clonal tree construction

https://bitbucket.org/edith_ross/onconem/src/76f7122a24c7539fbc29e6589b86110efbf7b13b?at=master

Binary matrix + estimation of FPR and FNR for each SNVS

Yes

Ross and Markowetz [114]

*

 BWA

DNA reads aligner

http://bio-bwa.sourceforge.net/bwa.shtml

fastq file + reference genome

No

Li [115]

*

Methylation

 Bismark

Aligner for bisulfite treated sequencing reads

https://www.bioinformatics.babraham.ac.uk/projects/bismark/

fastq files

No

Krueger and Andrews [83]

**

RNA-seq

 Granatum

Graphical pipeline for scRNA-seq analysis

http://garmiregroup.org/granatum/app

Expression matrix and sample metadata

Yes

Zhu et al. [56]

*****

 Monocle2

Pseudo-time construction using DDRTree

http://cole-trapnell-lab.github.io/monocle-release/articles/v2.0.0

Expression matrix and sample metadata

Yes

Trapnell et al. [57]

*

 scLVM

Subpopulation detection

https://github.com/PMBio/scLVM

Expression matrix

Yes

Buettner et al. [58]

*

 PseudoGP

Probabilistic pseudotime for single-cell RNA-seq data

https://github.com/kieranrcampbell/pseudogp

Expression matrix

Yes

Campbell et al. [116]

*

 SPADE

Cell hierarchy inference

http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html

Expression matrix

Yes

Anchang et al. [60]

*

 STAR

RNA-seq reads aligner

https://github.com/alexdobin/STAR

Fast

No

Dobin et al. [117]

**

CNV

 InferCNV

Average gene expression on large genomic regions

https://github.com/broadinstitute/inferCNV

Gene expression matrix

Yes

Patel et al. [63]

**

 ECdetect

Detection of extrachromosomal DNA

https://github.com/virajbdeshpande/AmpliconArchitect

Bam file

Yes

Turner et al. [118]

*

 CNVkit

Detection of CNV from DNA sequencing

https://github.com/etal./cnvkit

BAM file + target regions (BED files)

No

Talevich et al. [119]

**

 SynthEx

Detection of copy number alteration and tumour heterogeneity profiling for whole genome and exome sequencing

https://github.com/ChenMengjie/SynthEx

Count data (bed files) + optional vcf files for tumor samples

No

Silva et al. [120]

**

 Ginkgo

Web platform for visualization and clustering

http://qb.cshl.edu/ginkgo

Bed files

Yes

 

*****

 MutSigCV 2.0

Eliminate false positive mutations in large datasets

http://archive.broadinstitute.org/cancer/cga/mutsig

Mutations for each sample + sequencing coverage

No

Lawrence et al. [121]

**

 HotNet2

Identify mutated subnetworks across pathways and protein complexes

http://compbio.cs.brown.edu/projects/hotnet2/

Mutation data + protein–protein interaction network

No

Leiserson et al. [122]

*

Proteomics

 Wishbone

Reconstructing bifurcating developmental trajectories of single-cells

https://www.c2b2.columbia.edu/danapeerlab/html/wishbone.html

tsv expression files

Yes

Setty et al. [123]

***

Multi-omics

 DeepCpG

Infer missing methylation states and expressive DNA motifs linked to methylation

https://github.com/PMBio/deepcpg

Methylation position file + ref genomes + fastq files

Yes

Angermueller et al. [87]

*

 SSrGE

Link gene expression with SNVs. Provide a pipeline to extract SNVs from scRNA-seq

https://github.com/lanagarmire/SSrGE

Expression matrix + binary matrix; fastq files

Yes

Poirion et al. [106]

*

Genetic architecture

 combinatorialHiC

Processing single cell combinatorial indexed Hi-C

https://github.com/VRam142/combinatorialHiC

fastq files + barcodes

Yes

Ramani et al. [124]

*

Others

 Integrate-neo

Gene fusion neoantigen discovering tool

https://github.com/ChrisMaherLab/INTEGRATE-Neo

fastq files (or tsv) + bedpe files + reference genomics

No

Zhang et al. [125]

*

 awesome-single-cell

Exhaustive community-driven list of single-cell analytical tools

https://github.com/seandavi/awesome-single-cell

N/A

Yes

N/A

*****

  1. Software, computational packages, and databases mentioned in the paper
  2. The accessibility of a tool is our evaluation of its user-friendliness towards bench scientists who are not necessarily computationally trained
  3. The accessibility ranges from “*” (least accessible) to “*****” (most accessible)