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 | N/A | Yes | Cao et al. [62] | *** | |
The Human Protein Atlas | Spatial distribution of protein expressions | Protein name | No | ***** | ||
Enrichr | Very complete meta-database | List of genes/proteins—BED file | No | Kuleshov et al. [110] | ***** | |
CIViC | Clinical interpretation of cancer variant | Gene or variant ID | No | Griffith et al. [111] | **** | |
MyGene2 | A portal for sharing health and genetic information | Genetic information | No | Xin et al. [112] | **** | |
Genome sequencing | ||||||
SCITE | Pseudo-temporal clonal tree construction | 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 | fastq file + reference genome | No | Li [115] | * | |
Methylation | ||||||
Bismark | Aligner for bisulfite treated sequencing reads | fastq files | No | Krueger and Andrews [83] | ** | |
RNA-seq | ||||||
Granatum | Graphical pipeline for scRNA-seq analysis | 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 | Expression matrix | Yes | Buettner et al. [58] | * | |
PseudoGP | Probabilistic pseudotime for single-cell RNA-seq data | 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 | Fast | No | Dobin et al. [117] | ** | |
CNV | ||||||
InferCNV | Average gene expression on large genomic regions | Gene expression matrix | Yes | Patel et al. [63] | ** | |
ECdetect | Detection of extrachromosomal DNA | Bam file | Yes | Turner et al. [118] | * | |
CNVkit | Detection of CNV from DNA sequencing | 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 | Count data (bed files) + optional vcf files for tumor samples | No | Silva et al. [120] | ** | |
Ginkgo | Web platform for visualization and clustering | Bed files | Yes | ***** | ||
MutSigCV 2.0 | Eliminate false positive mutations in large datasets | Mutations for each sample + sequencing coverage | No | Lawrence et al. [121] | ** | |
HotNet2 | Identify mutated subnetworks across pathways and protein complexes | 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 | 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 | Expression matrix + binary matrix; fastq files | Yes | Poirion et al. [106] | * | |
Genetic architecture | ||||||
combinatorialHiC | Processing single cell combinatorial indexed Hi-C | fastq files + barcodes | Yes | Ramani et al. [124] | * | |
Others | ||||||
Integrate-neo | Gene fusion neoantigen discovering tool | 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 | N/A | Yes | N/A | ***** |