Manoj Kumar Valluru's repositories
APAeval
Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples
awesome-biological-image-analysis
A curated list of softwares, tools, pipelines, plugins etc. for image analysis related to biological questions.
BrindlePlots.jl
Visualization package for Whippet.jl
cellxgene_VIP
Enable cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format.
circRNA_finder
Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).
CLEAR
direct comparison of circular and linear RNA expression
clinker
Gene cluster comparison figure generator
cv
Dr Manoj K Valluru - Curriculum vitae
DECODE
This is the official implementation of our preprint "Deep learning enables fast and dense single-molecule localization with high accuracy"
EVE
Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.
gget
🧬 gget enables efficient querying of genomic reference databases
Giotto
Single-cell spatial analysis toolbox
MAAPER
Model-based analysis of APA using 3' end-linked reads
MERmaid
WebGL-based viewer for spatially-resolved transcriptomics data
ORQAS
ORF Quantification pipeline for Alternative Splicing
prettymaps
A small set of Python functions to draw pretty maps from OpenStreetMap data. Based on osmnx, matplotlib and shapely libraries.
proteinnet
Standardized data set for machine learning of protein structure
PSI-Sigma
PSI-Sigma
pytorch_fnet
Three dimensional cross-modal image inference
rna-tools
🔧rna-tools (prev. rna-pdb-tools): a toolbox to analyze sequences, structures and simulations of RNA - docs @ http://rna-tools.rtfd.io
sheffield-bioinformatics-core.github.io
Website for The University of Sheffield Bioinformatics Core
tellervo
Organoid Classifier (Yolov5)
vast-tools
A toolset for profiling alternative splicing events in RNA-Seq data.