Xianfeng Li's repositories
apa
apa: research platform for the study of alternative polyadenylation, expressRNA.org
ATAC-pipe
Analysis pipeline for ATAC-seq Data
bms038_analysis
Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization
circM
Scripts for merging circRNA prediction output
circscan
Discovering the Circular RNA Interactions with RNA-binding Proteins and Ribosomes
CISD
Chromatin Interaction Site Detector
ComplexHeatmap
make complex heatmaps as well as self define annotation graphics
cworld-dekker
perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
extract-transcript-regions
For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and CDS).
ggstatsplot
Collection of functions to enhance ggplot2 plots with results from statistical tests.
GTExV6PRareVariation
Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript
HOME
DMR Identification Tool
iDeepS
inferring sequence-structure motifs using deep learning
imrep-project
Scripts and commands we used in our study : Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing
leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
LncPipe
A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
Mallm-et-al-processing-scripts
A public repository to reproduce data processing and analysis for Mallm, Iskar, Ishaque et. al. 2018
MethylDackel
A (mostly) universal methylation extractor for BS-seq experiments.
NGS_data_sets
Collection profiles from public project
phenopredict
Use gene expression to predict phenotype sample information
PSYCHIC
Code for finding putative enhancers using Hi-C data
RNAcommender
genome-wide recommendation of RNA-protein interactions
SEASTAR
SEASTAR - Systematic Evaluation of Alternative transcription STArt site in RNA
simple_sv_annotation
Simplify snpEff annotations for interesting cases
sports1.0
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
StructuralVariantAnnotation
R package designed to simplify structural variant analysis
TargetSeq-QC
This is a perl script which can generate some statistics on the Targeted re-sequencing bam file.
useful_scripts
There are some useful scripts powered by ChangeGene LLC.
vdjdb-db
Git-based TCR database storage & management. Submissions welcome!