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Top bioinformatics tools ranked by usage across 144 tools.
| Rank | Tool | Usage | Trend | ||
|---|---|---|---|---|---|
| 30 | cell2location | Transcriptomics | Transcriptomics | 35.92 | +8% |
| 97 | CellTypist | Transcriptomics | Transcriptomics | 26.7 |
Data as of: Apr 12, 2026
| 32 | clusterProfiler | Transcriptomics | Transcriptomics | 35.86 | +8% |
| 29 | Corset | Transcriptomics | Transcriptomics | 36.4 | +8% |
| 21 | Cufflinks | Transcriptomics | Transcriptomics | 38.8 | +8% |
| 98 | Cuffmerge | Transcriptomics | Transcriptomics | 26.7 | +3% |
| 33 | CytoTRACE -- Predicting Differentiation State from scRNA-seq | Transcriptomics | Transcriptomics | 35.86 | +8% |
| 59 | Decoupler -- Biological Activity Inference from Omics Data | Transcriptomics | Transcriptomics | 35.74 | +8% |
| 73 | demuxlet / freemuxlet (popscle) | Transcriptomics | Transcriptomics | 29.7 | +3% |
| 1 | DESeq2 | Transcriptomics | Transcriptomics | 68.08 | +15% |