Python-based applications use isoform.py for common functions. The genomikon repo contains a couple of faster implementations in the isoformer directory. Data collection is described in datacore2024/project_splicing. The 1045 genes of the smallgenes dataset. See the models directory for standard models and modelbuilder for how to build the models.

The outputs of ISOdb are presented in two levels: (1) sample level, including metainformation, long read distribution, isoform numbers, and AS events of each sample; (2) gene level, including the total isoform, novel isoform number, novel AS number, and isoform visualisation for …

To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution.

By examining isoform-level expression changes, researchers can identify and characterize specific isoforms that may have unique roles in cellular processes, such as isoform-specific protein-protein interactions or protein functions.

For over half of gene-specific isoform pairs in which each isoform exhibited at least one interaction, the comparative interactome profiles differ by 50% or more, suggesting that distinct isoforms engage in differential sets of interactions leading to distinct functional differences.

IsoVis displays the exonic structures of isoforms from GFF, GTF or BED files as an isoform stack. It can also show isoform expression data from CSV or tab-separated text files as a heatmap. Reference data including the canonical ENSEMBL transcript, open reading frames and encoded protein features are integrated with the isoform information.

IsONform generates isoforms out of clustered and corrected long reads. For this a graph is built up using the networkx api and different simplification strategies are applied to it, such as bubble popping and node merging. The algorithm uses spoa to generate the final isoforms.

Protein isoforms are different forms of a protein that arise from the same gene due to variations in splicing, post-translational modifications, or genetic mutations. These isoforms can exhibit distinct functional properties, structures, or interactions, contributing to the …

Isoform information includes both manually reviewed sequences, which may have specific names, functional information and experimental evidence associated with them, and also automatic gene-centric isoform mappings from eukaryotic reference proteome sequences.

In this paper, we present a large-scale comparative study among RNA-seq, NanoString, array-based, and RT-qPCR platforms using 46 cancer cell lines across different cancer types. The goal is to understand and evaluate the calibers of the platforms for measuring gene and isoform expressions in cancer studies.