ustcahwry

ustcahwry's Stars

• vaquerizaslab/fanc

  FAN-C: Framework for the ANalysis of C-like data

  Language:Python10414

• krishna-shrinivas/2019_Shrinivas_Sabari_enhancer_features

  Code relating to paper titled "Enhancer features that drive formation of transcriptional condensates"

  Language:Python21

• al-mcintyre/CovFuzze

  Script for plotting coverage and peaks for multiple replicates

  Language:Python93

• deeptools/pyGenomeTracks

  python module to plot beautiful and highly customizable genome browser tracks

  Language:Python741111

• crazyhottommy/ChIP-seq-analysis

  ChIP-seq analysis notes from Ming Tang

  Language:Python715293

• ParkerLab/ataqv

  A toolkit for QC and visualization of ATAC-seq results.

  Language:C++6310

• kundajelab/atac_dnase_pipelines

  ATAC-seq and DNase-seq processing pipeline

  Language:Python16081

• mikelove/bioc-refcard

  Bioconductor cheat sheet

  Language:R18565

• lijingya/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

  Language:R616

• dnaase/Bis-tools

  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )

  Language:Java2923

• daler/metaseq

  Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

  Language:Python8736

• bdo311/metagene-maker

  makes metagene plots for next-gen sequencing data over given regions

  Language:Python54

• charite/topodombar

  Phenotypic analysis of microdeletions and toplogical chromosome domain boundaries

  Language:Python14

• kundajelab/chromovar3d

  Code from the chromatin variation 3d project

  Language:JavaScript63

• 3DGenomes/TADbit

  TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

  Language:Python9961

• biocoder/Perl-for-Bioinformatics

  An attempt to help anyone interested in using Perl for Bioinformatics

  Language:Python3331

• dphansti/mango

  chia pet analysis software

  Language:C++2315

• griffithlab/rnaseq_tutorial

  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

  Language:R1.3k617

• nservant/HiC-Pro

  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

  Language:Python375181

• cs109/content

  Official content for Harvard CS109

  Language:Jupyter Notebook1.8k1.6k

• lulab/COME_beta

  Coding potential from multiple features

  Language:Shell1

• YeoLab/clipper

  A tool to identify CLIP-seq peaks

  Language:Python6241

• www-bioinfo-org/CNCI

  Coding-Non-Coding Index (CNCI)

  Language:Python3734

• frankMusacchia/Annocript

  Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript

  Language:Perl5328

• trinityrnaseq/trinityrnaseq

  Trinity RNA-Seq de novo transcriptome assembly

  Language:Perl810316

• alexdobin/STAR

  RNA-seq aligner

  Language:C1.8k498

• jbmouret/matplotlib_for_papers

  Handout for the tutorial "Creating publication-quality figures with matplotlib"

  Language:Jupyter Notebook2.1k297

• freeCodeCamp/freeCodeCamp

  freeCodeCamp.org's open-source codebase and curriculum. Learn to code for free.

  Language:TypeScript394k36.3k

• julycoding/The-Art-Of-Programming-By-July-2nd

  本项目曾冲到全球第一，干货集锦见本页面最底部，另完整精致的纸质版《编程之法：面试和算法心得》已在京东/当当上销售

  Language:C21.3k7.1k

• ipython/ipython

  Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

  Language:Python16.2k4.4k