ArticleBioinformatics advances2025
WebCMap: an R package for high-throughput connectivity analysis within the CMap framework.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed.
- DRIVE: a comprehensive resource deciphering drug-induced transcriptomic and splicing response in cancer cell.Neoplasia (New York, N.Y.) · 2026Article
- The cell-type specific interaction based drug repurposing for psychiatric disorders.Translational psychiatry · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Experimentally generated drug-induced transcriptomic signatures are valuable resources to infer candidate drugs for unseen transcriptomes. The Connectivity Map (CMap) includes over 720 000 compound-induced signatures and has been widely used in drug repurposing. However, the computational resources required for an unbiased screen across all these signatures, along with the inconsistent results from different methods, presented huge challenges for the connectivity analyses. Results: In this study, we developed WebCMap, an R package to search for candidate compounds with similar or reverse activities across all CMap drug-induced signatures. WebCMap implements six widely used methods and a meta-score to evaluate the consistency among these methods. Through a web-accelerated framework, pre-calculated statistics for the permutation test, and multi-core parallelization, WebCMap enables fast screening and retrieval of the results on personal computers within a reasonable time. Availability and implementation: WebCMap is available at https://github.com/geneprophet/WebCMap.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.