Pinned Repositories
acfs
A pipeline for de novo circRNA identification
ancestry
program to estimate admixture coefficients from individual genotype or sequence data
APAlyzer
APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is comparison of sequencing reads in regions demarcated by high quality polyadenylation sites (PASs) annotated in the PolyA_DB database (http://exon.njms.rutgers.edu/polya_db/v3/). The current version (v3.0) uses RNA-seq data to examine APA events in 3’ untranslated regions (3’UTRs) and in introns. The coding regions are used for gene expression calculation.
benchmarking_scripts
Repository to benchmark algorithms for determining expressed full length mRNA splice forms from RNA-seq data.
lncRNA-mRNA-interaction
Collected methods of lncRNA & mRNA interaction
lncRNA-screen
lncRNA-screen
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
spladder
Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
swDMR
A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
VisualisingGenomicsData
R examples to visualise genomics data
xflicsu's Repositories
xflicsu/swDMR
A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
xflicsu/HiC_tools
A collection of tools for Hi-C data analysis
xflicsu/academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
xflicsu/Alternative-Splicing-Tools
A list of alternative splicing analysis resources
xflicsu/ATAC-seq
Basic workflow for ATAC-seq analysis
xflicsu/CALDER
xflicsu/CellChat
R toolkit for inference and analysis of cell-cell communication from single-cell data
xflicsu/CHOIR
CHOIR : Clustering Hierarchy Optimization by Iterative Random forests (www.CHOIRclustering.com)
xflicsu/colon-dna-topology
xflicsu/COVID-19-RNA-Seq-datasets
A repository for sharing information on available COVID-19 RNA-Seq datasets
xflicsu/DNBelab_C_Series_HT_scRNA-analysis-software
An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
xflicsu/ESD
Genomic variations of multi-grade esophageal squamous dysplasia
xflicsu/gpt_academic
为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, moss等。
xflicsu/HiTea
computational tool to identify trasposable element insertions using Hi-C data
xflicsu/human-atac
Code for demultiplexing and cell barcode assignment for sci-ATAC3 runs
xflicsu/hyperclust
xflicsu/lungATAC_analysis_code
xflicsu/MosaicForecast
A mosaic detecting software based on phasing and random forest
xflicsu/Nuc-PF
Codes of Dynamic nucleosome landscape elicits a novel noncanonical GATA2 pioneer model
xflicsu/Oslops
Combine the pipeline of CYCLOPS and Oscope for ordering human sampls
xflicsu/parallel-fastq-dump
parallel fastq-dump wrapper
xflicsu/PReLIM
Python package for imputing missing CpG methylation data at the read level
xflicsu/RADAR
RADAR is devised to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.
xflicsu/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
xflicsu/seatac
xflicsu/SequencingCancerFinder
xflicsu/Sierra
Discover differential transcript usage from polyA-captured single cell RNA-seq data
xflicsu/single-cell-papers
Database for collecting and curating scientific papers related to single-cell and spatial transcriptomics sequencing.
xflicsu/split-seq-pipeline
xflicsu/TF-COMB
Transcription Factor Co-Occurrence using Market Basket analysis