MINTIE is a tool for identifying novel, rare cryptic variants in cancer RNA-seq data. Please see the wiki for installation and running instructions.
Oshlack / MINTIE
Licence: MIT License
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
Stars: ✭ 24
Programming Languages
Labels
Projects that are alternatives of or similar to MINTIE
arriba
Fast and accurate gene fusion detection from RNA-Seq data
Stars: ✭ 162 (+575%)
Mutual labels: rna-seq, cancer, structural-variation, gene-fusions
pipeline-pinfish-analysis
Pipeline for annotating genomes using long read transcriptomics data with pinfish
Stars: ✭ 27 (+12.5%)
Mutual labels: rna-seq, transcriptomics
pychopper
A tool to identify, orient, trim and rescue full length cDNA reads
Stars: ✭ 74 (+208.33%)
Mutual labels: rna-seq, transcriptomics
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Stars: ✭ 137 (+470.83%)
Mutual labels: rna-seq, transcriptomics
MetaOmGraph
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
Stars: ✭ 30 (+25%)
Mutual labels: rna-seq, transcriptomics
dee2
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Stars: ✭ 32 (+33.33%)
Mutual labels: rna-seq, transcriptomics
TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Stars: ✭ 18 (-25%)
Mutual labels: rna-seq, transcriptomics
IsoQuant
Reference-based transcript discovery from long RNA read
Stars: ✭ 26 (+8.33%)
Mutual labels: rna-seq, transcriptomics
squid
SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
Stars: ✭ 37 (+54.17%)
Mutual labels: rna-seq, structural-variation
alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Stars: ✭ 78 (+225%)
Mutual labels: rna-seq, transcriptomics
SVCollector
Method to optimally select samples for validation and resequencing
Stars: ✭ 20 (-16.67%)
Mutual labels: structural-variation
velodyn
Dynamical systems methods for RNA velocity analysis
Stars: ✭ 16 (-33.33%)
Mutual labels: rna-seq
civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
Stars: ✭ 49 (+104.17%)
Mutual labels: cancer
rare-disease-wf
(WIP) best-practices workflow for rare disease
Stars: ✭ 47 (+95.83%)
Mutual labels: rare-disease
picardmetrics
🚦 Run Picard on BAM files and collate 90 metrics into one file.
Stars: ✭ 38 (+58.33%)
Mutual labels: rna-seq
CoNekT
CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
Stars: ✭ 17 (-29.17%)
Mutual labels: rna-seq
gene-oracle
Feature extraction algorithm for genomic data
Stars: ✭ 13 (-45.83%)
Mutual labels: rna-seq
EWCE
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
Stars: ✭ 30 (+25%)
Mutual labels: transcriptomics
Front-End
Federated Learning based Deep Learning. Docs: https://fets-ai.github.io/Front-End/
Stars: ✭ 35 (+45.83%)
Mutual labels: cancer
Note that the project description data, including the texts, logos, images, and/or trademarks,
for each open source project belongs to its rightful owner.
If you wish to add or remove any projects, please contact us at [email protected].