yjzhang2013

ScanExitron

A computational workflow for exitron splicing identification

shiny-apps

R Shiny apps

ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization

HRT_Atlas

Web-based tools to search housekeeping genes and tissue specific reference transcripts

atac-seq-pipeline

ENCODE ATAC-seq pipeline

tcga_example

shiny-examples

ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

kallisto

Near-optimal RNA-Seq quantification

ggforestplot

An R package to create forestplots of measures of effects with their confidence intervals.

IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)

CSI

Complementary Sequence Index (CSI)

find_circ

tools to find circRNAs in RNA-seq data

PAIRADISE

Paired Replicate Analysis of Allelic Differential Splicing Events

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

chilin

ChIP-seq DC and QC Pipeline

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

BiocWorkshops2019

The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball:

OrchestratingSingleCellAnalysis

Content for the OSCA Book.

SRAdbV2

R Interface to the NCBI SRA metadata

ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes

motifmatchr

Fast motif matching in R

pepatac

A modular, containerized pipeline for ATAC-seq data processing

intropolis

Exon-exon splice junctions across SRA

snaptron

fast webservices based query tool for large sets of genomic features

ascot

ASCOT - Alternative Splicing and Gene Expression Summaries of Public RNA-Seq Data

rhdf5

Package providing an interface between HDF5 and R

ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

clipseqtools

A suite for the analysis of CLIP-Seq datasets.