gosianow

gosianow's Stars

• google-deepmind/alphafold

  Open source code for AlphaFold.

  Language:Python12.7k2268592.3k

• yihui/knitr

  A general-purpose tool for dynamic report generation in R

  Language:R2.4k1161.8k880

• lh3/seqtk

  Toolkit for processing sequences in FASTA/Q formats

  Language:C1.4k62174306

• stardist/stardist

  StarDist - Object Detection with Star-convex Shapes

  Language:Python91527228220

• welch-lab/liger

  R package for integrating and analyzing multiple single-cell datasets

  Language:R3892218978

• dylkot/cNMF

  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

  Language:Jupyter Notebook27169657

• constantAmateur/SoupX

  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

  Language:R257614735

• moldach/project-directory

  Setting up a new project directory in the terminal or R

  2397023

• docopt/docopt.R

  Command-line interface description language for R (http://docopt.org)

  Language:R210153517

• joiningdata/lollipops

  Lollipop-style mutation diagrams for annotating genetic variations.

  Language:Go182187370

• dviraran/xCell

  Cell types enrichment analysis

  Language:HTML18198161

• marakeby/pnet_prostate_paper

  P-NET, Biologically informed deep neural network for prostate cancer classification and discovery

  Language:HTML14911858

• campbio/celda

  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

  Language:R148710428

• czbiohub-sf/scell_lung_adenocarcinoma

  This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

  Language:HTML1439491

• carmonalab/UCell

  Gene set scoring for single-cell data

  Language:R13554016

• theislab/sfaira

  data and model repository for single-cell data

  Language:Python134835111

• Thie1e/cutpointr

  Optimal cutpoints in R: determining and validating optimal cutpoints in binary classification

  Language:R8544713

• BostonGene/Kassandra

  Bostongene cell deconvolution algorithm from RNAseq

  Language:Jupyter Notebook50297

• AlexandrovLab/SigProfilerAssignment

  Assignment of known mutational signatures to individual samples and individual somatic mutations

  Language:Python4636910

• decomverse/ACTIONet

  ACTIONet single-cell analysis framework

  366307

• matanhofree/crc-immune-hubs

  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organized multicellular immune hubs in human colorectal cancer"

  Language:Jupyter Notebook36544

• kkdey/CountClust

  A R package for Grade of Membership model and Visualization of counts data:

  Language:R3172911

• Sage-Bionetworks/CMSclassifier

  Language:R2824817

• peterawe/CMScaller

  Language:R265717

• pbnjay/lollipops

  This is the development fork - Stable code has been moved to ==>

  Language:Go22109

• rockdeme/chrysalis

  Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.

  Language:Jupyter Notebook15230

• Sage-Bionetworks/crcsc

  CRC Subtyping Consortium

  Language:R1223117

• TAPE-Lab/Qin-CardosoRodriguez-et-al

  Scripts and notebooks for Qin & Cardoso Rodriguez et al

  Language:Jupyter Notebook9102

• dpcook/emp_programs

  Code used in the manuscript "Transcriptional census of epithelial-mesenchymal plasticity in cancer"

  Language:R4110

• AlexandrovLab/SigProfilerAssignmentR

  R wrapper for utilizing the SigProfilerAssignment framework

  Language:R1140