Pangolin

Pan.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.

Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.

[@crazyhottommy](https://github.com/crazyhottommy)'s notes on various steps and considerations when doing RNA-seq analysis.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

General-purpose RNA language model with 650M parameters pretrained on 36M non-coding RNA sequences, achieving strong generalization on structure prediction tasks including secondary structure prediction, splice-site prediction, mean ribosome loading, and ncRNA classification (lbcb-sci, 165+ stars, Apache-2.0)