vickyrev

vickyrev's Stars

• BostonGene/MFP

  Mollecular Functional Portraits

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• siyao-liu/MultiK

  MultiK is a data-driven tool that objectively assesses the optimal number(s) of clusters based on the concept of consensus clustering via a multi-resolution perspective.

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• califano-lab/PISCES

  R package for Protein activity analysis of single-cell RNAseq.

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• krumsieklab/maplet

  R statistical toolbox for metabolomics

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• immunogenomics/presto

  Fast Wilcoxon and auROC

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• sqjin/CellChat

  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

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• aertslab/SCENIC

  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

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• nf-core/atacseq

  ATAC-seq peak-calling and QC analysis pipeline

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• theislab/cellrank

  CellRank: dynamics from multi-view single-cell data

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• broadinstitute/Celligner_ms

  Code related to the Celligner manuscript

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• saeyslab/nichenetr

  NicheNet: predict active ligand-target links between interacting cells

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• theislab/scvelo

  RNA Velocity generalized through dynamical modeling

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• quadbio/simspec

  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

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• facebookresearch/PoincareMaps

  The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

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• velocyto-team/velocyto.R

  RNA velocity estimation in R

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• soedinglab/merlot

  Reconstruct the lineage topology of a scRNA-seq differentiation dataset.

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• GuoliangLi-HZAU/BatMeth2

  BS-seq analysis pipeline

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• apptainer/singularity

  Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.

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• harvardinformatics/ATAC-seq

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• williamritchie/IRFinder

  Detecting intron retention from RNA-Seq experiments

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• marislab/create-pptc-pdx-oncoprints

  As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

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• AlexsLemonade/OpenPBTA-analysis

  The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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• bcbio/bcbio_validations

  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

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• methodistsmab/CCCExplorer

  Paper - Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model

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• LSun/cashr

  `cashr`: Solve the correlated Empirical Bayes Normal Means problem, with applications to large-scale multiple testing

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• shenorrLabTRDF/bseqsc

  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline

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• xuranw/MuSiC

  Multi-subject Single Cell Deconvolution

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• jasongfleischer/Predicting-age-from-the-transcriptome-of-human-dermal-fibroblasts

  Code to generate Figure 2 of the paper "Predicting age from the transcriptome of human dermal fibroblasts" from the FPKM tables

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• PoisonAlien/maftools

  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

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• NKI-GCF/XenofilteR

  Filtering of PDX samples for mouse derived reads

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