candacechan

candacechan's Stars

• prasmussen/gdrive

  Google Drive CLI Client

  Language:Go9k2235941.2k

• zhixuhao/unet

  unet for image segmentation

  Language:Jupyter Notebook4.5k1022342k

• JunMa11/SegLossOdyssey

  A collection of loss functions for medical image segmentation

  Language:Python3.8k9847596

• life4/textdistance

  📐 Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.

  Language:Python3.4k640250

• seandavi/awesome-single-cell

  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

  3.1k24823963

• deeptools/pyGenomeTracks

  python module to plot beautiful and highly customizable genome browser tracks

  Language:Python75531208111

• hms-dbmi/UpSetR

  An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

  Language:R75238233152

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R5811215364

• krassowski/complex-upset

  A library for creating complex UpSet plots with ggplot2 geoms

  Language:Jupyter Notebook455917728

• Teichlab/scg_lib_structs

  Collections of library structure and sequence of popular single cell genomic methods

  Language:HTML416311387

• calico/basenji

  Sequential regulatory activity predictions with deep convolutional neural networks.

  Language:Python39130169120

• CamDavidsonPilon/tdigest

  t-Digest data structure in Python. Useful for percentiles and quantiles, including distributed enviroments like PySpark

  Language:Python381123654

• MarioniLab/miloR

  R package implementation of Milo for testing for differential abundance in KNN graphs

  Language:R335924422

• reneshbedre/bioinfokit

  Bioinformatics data analysis and visualization toolkit

  Language:Python33486277

• PhanstielLab/plotgardener

  Language:R29989028

• shenlab-sinai/ngsplot

  Quick mining and visualization of NGS data by integrating genomic databases

  Language:R252259465

• scverse/scirpy

  A scanpy extension to analyse single-cell TCR and BCR data.

  Language:Python2141028834

• mhammell-laboratory/TEtranscripts

  A package for including transposable elements in differential enrichment analysis of sequencing datasets.

  Language:Python2131819629

• broadinstitute/ABC-Enhancer-Gene-Prediction

  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

  Language:Python1991410059

• AlexandrovLab/SigProfilerExtractor

  SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

  Language:Python1512420851

• churchmanlab/genewalk

  GeneWalk identifies relevant gene functions for a biological context using network representation learning

  Language:Python12873415

• YuLab-SMU/ggbreak

  :broken_heart: An implementation of scale functions for setting axis breaks of a 'gg' plot.

  Language:R1277524

• PortableApps/Toucan

  sync, backup and secure, all in one place

  Language:C++126124723

• puolival/multipy

  Multiple hypothesis testing in Python

  Language:Python1032723

• open2c/pairtools

  Extract 3D contacts (.pairs) from sequencing alignments

  Language:Python971115632

• vanheeringen-lab/ANANSE

  Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

  Language:Python77510816

• ParkerLab/ataqv

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

  Language:C++6482810

• mpg-age-bioinformatics/AGEpy

  Bioinformatics tools for Python

  Language:Python236123

• kimmo1019/hicGAN

  Hi-C data super-resolution with generative adversarial networks

  Language:Jupyter Notebook15259