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anomalydetection

Anomaly Detection with R

apapathway

apasurvey

A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data

astrap

AStrap: Identification of alternative splicing from transcript sequences without a reference genome

bayesspace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

bmilab.github.io

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movapa

pascca

Cluster analysis of replicated alternative polyadenylation data using shrinkage canonical correlation analysis

pias

a web-based interactive platform for integrative analysis of multi-source single-cell RNA-seq datasets

polyacode

polyatailor

PolyAtailor is a user-friendly R package for measuring poly(A) tail length from NGS-based short-read and PacBio-based long-read sequencing data. Core functions of Tail_map and Tail_scan provided in PolyAtailor can profile tails with or without using a reference genome. PolyAtailor can identify multiple tails in a read, with detailed information of tail type, tail position, tail length and tail sequence. PolyAtailor also integrates rich functions for downstream analyses and visualization of poly(A) tails and poly(A) sites.

readme

README文件语法解读，即Github Flavored Markdown语法介绍

root_scapa_atlas

scapamod

scapatrap

schinter

scHinter: Imputing dropout events for single-cell RNA-seq data with limited sample size

sclapa

scline

scnpf

An integrative framework assisted by network propagation and network fusion for pre-processing of single-cell RNA-seq data

spvapa

spvAPA is a simple R package for the imputation and supervised analysis of sparse APA matrices. spvAPA can recover APA signatures from highly sparse and noisy data, identify APA features that differentiate cell types or spatial morphologies, improve the visualization of single-cell data, and uncover cell subpopulations.

stapaminer

synthetic-polya-site-data

Based on real rice poly(A) data set, we used a two-step process to generate synthetic data that have the same distributions of abundance of poly(A) sites derived from the rice data.

targetfinder

Plant small RNA target prediction tool

test_git

tsapa

TSAPA: Identificantion of tissue-specific alternative polyadenylation sites

vizapa

The vizAPA package is a comprehensive package for Visualization of dynamics of alternative PolyAdenylation in single cells. vizTracks to plot gene model, pAs and BAM coverages, vizStats to summarize pA usages across cell categories, vizUMAP to plot 2D-embeddings, vizAPAmarkers to visualize APA markers across cell categories, etc.