Pan.bio
https://bio.tools/pan_bioPan.bio is a cloud genomics platform for pipeline execution, exploratory analysis, and clinical variant interpretation. Workflows runs validated Nextflow and nf-core pipelines including Sarek, rnaseq, scrnaseq, mag, ampliseq, chipseq and atacseq without local installation. Notebooks provides Python and R sessions with a preinstalled bioinformatics stack, importing public data from GEO, SRA and IPG by accession and reading Workflows outputs directly. VAIC applies ACMG/AMP variant classification with gene-specific rule sets from CanVIG-UK and ClinGen ENIGMA, with automated evidence criteria implemented for BRCA1 and BRCA2. Cohorts provides federated analysis of patient data within a Trusted Research Environment.
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Related resources
Pangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.
A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.
Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).
Thoa is a cloud bioinformatics platform. Write your Nextflow or Snakemake pipeline, point it at your data, and Thoa handles the rest: provisioning VMs (up to 12TB RAM), resolving dependencies, managing execution. No cloud expertise needed. Every job captures its full context:data, software versions, environment, machine specs, as a reproducibility artifact. Share it with a colleague and they can view or re-run the analysis without an account. Key features: AI debugger that fixes environment and dependency issues in real time. Pipeline tracking with per-step telemetry. if step 47 of 200 fails, re-run from there, not from scratch. One-click data sharing without registration. AI-assisted workflow creation from plain English. Free tier available. Starter $35/mo, Pro $109/mo, Team $480/mo. Zero-egress storage. Based in Zug, Switzerland. thoa.io
Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.
Deep learning-based variant caller