Pinned Repositories
ADmiRE
ADmiRE: Annotative Database of miRNA Elements
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
APA-Scan
Detection and visualization of annotated and potential Alternative Polyadenylation events
ENCODE_miRNA_pipeline
mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
NCRF
Cancer metastasis detection with neural conditional random field (NCRF)
Serum_miRNA_GENES
smallrnaseq
small rna-seq analysis package
smallseq
Pipeline to analyze small RNAs from single-cells
srnaseq
small RNA-Seq pipeline (paired-end/single-end)
vallurumk's Repositories
vallurumk/APA-Scan
Detection and visualization of annotated and potential Alternative Polyadenylation events
vallurumk/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
vallurumk/awesome-biological-image-analysis
A curated list of softwares, tools, pipelines, plugins etc. for image analysis related to biological questions.
vallurumk/BrindlePlots.jl
Visualization package for Whippet.jl
vallurumk/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.
vallurumk/circRNA_finder
Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).
vallurumk/circtools
circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.
vallurumk/CLEAR
direct comparison of circular and linear RNA expression
vallurumk/clinker
Gene cluster comparison figure generator
vallurumk/cv
Dr Manoj K Valluru - Curriculum vitae
vallurumk/DECODE
This is the official implementation of our preprint "Deep learning enables fast and dense single-molecule localization with high accuracy"
vallurumk/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.
vallurumk/gget
🧬 gget enables efficient querying of genomic reference databases
vallurumk/Giotto
Single-cell spatial analysis toolbox
vallurumk/GraphAlignmentViewer
vallurumk/MAAPER
Model-based analysis of APA using 3' end-linked reads
vallurumk/MERmaid
WebGL-based viewer for spatially-resolved transcriptomics data
vallurumk/mirtrace
miRTrace
vallurumk/novosparc
vallurumk/ORQAS
ORF Quantification pipeline for Alternative Splicing
vallurumk/prettymaps
A small set of Python functions to draw pretty maps from OpenStreetMap data. Based on osmnx, matplotlib and shapely libraries.
vallurumk/proteinnet
Standardized data set for machine learning of protein structure
vallurumk/PSI-Sigma
PSI-Sigma
vallurumk/pytorch_fnet
Three dimensional cross-modal image inference
vallurumk/rajlabimagetools
vallurumk/rna-tools
🔧rna-tools (prev. rna-pdb-tools): a toolbox to analyze sequences, structures and simulations of RNA - docs @ http://rna-tools.rtfd.io
vallurumk/sheffield-bioinformatics-core.github.io
Website for The University of Sheffield Bioinformatics Core
vallurumk/tellervo
Organoid Classifier (Yolov5)
vallurumk/vast-tools
A toolset for profiling alternative splicing events in RNA-Seq data.
vallurumk/workshop-spatial