scrna-seq-analysis

Silhouette plot labels clusters by integers from 1 - # of clusters. If clusters are named, or numbered differently (Seurat counts clusters from zero because apparently they forgot they weren't Python?), this creates a great deal of confusion.

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IMB-Computational-Genomics-Lab / ascend

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R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

r scrnaseq singlecell scrna-seq-analysis rpackages

Updated Aug 28, 2019
R

quon-titative-biology / scAlign

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A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

scrna-seq single-cell single-cell-genomics scrna-seq-analysis human-cell-atlas

Updated Mar 1, 2020
R

dpeerlab / Harmony

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Harmony framework for connecting scRNA-seq data from discrete time points

scrna-seq mnn batch-correction scrna-seq-analysis developmental-trajecotries

Updated May 10, 2020
Jupyter Notebook

paulranum11 / SPLiT-Seq_demultiplexing

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An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

scrna-seq single-cell fastq demultiplexing single-cell-rna-seq single-cell-analysis single-cell-omics scrna-seq-analysis single-cell-sequencing split-seq

Updated Feb 23, 2020
Python

jyyulab / NetBID

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Data-driven Network-based Bayesian Inference of Drivers

bayesian-inference r-package network-analysis rna-seq-analysis scrna-seq-analysis

Updated Apr 22, 2020
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northstaratlas / northstar

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Single cell type annotation guided by cell atlases, with freedom to be queer

clustering scrna-seq singlecell scrna-seq-analysis cell-atlas leidenalg

Updated May 21, 2020
Python

JDBLab / Pancreas_ductal_scRNAseq

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The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysis of the human pancreatic ductal progenitor cell niche

10xgenomics pancreas scrna-seq-analysis

Updated May 4, 2020
R

juliendelile / Antler

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R package for single-cell RNA-sequencing analysis

bioinformatics dimensionality-reduction scrna-seq-analysis

Updated May 16, 2020
R

milescsmith / ReducedHeat

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Display gene expression along a given reduced dimension on a heatmap

heatmap tsne umap seurat scrna-seq-analysis tsne-heatmaps

Updated Feb 12, 2020
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rfechtner / pypairs

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PyPairs - A python scRNA-Seq classifier

bioinformatics bioinformatics-algorithms single-cell-analysis scrna-seq-analysis

Updated Feb 29, 2020
Python

quon-titative-biology / scBFA

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Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data

scrna-seq single-cell single-cell-genomics single-cell-atac-seq scrna-seq-analysis human-cell-atlas

Updated Mar 17, 2020
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KorkinLab / DUSC

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Deep Unsupervised Single-cell Clustering (DUSC) is a hybrid approach for cell type discovery in scRNA-seq data.

single-cell-rna-seq single-cell-analysis scrna-seq-analysis sc-rna-seq

Updated Apr 23, 2019
Python

JulianSpagnuolo / adtseq

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adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data

scrna-seq 10x 10x-genomics scrnaseq drop-seq dropseq dropseqtools scrna-seq-analysis citeseq cite-seq

Updated Jun 21, 2019
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tarot0410 / BREMSC

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Novel joint clustering method with scRNA-seq and CITE-seq data

clustering-methods scrna-seq-analysis cite-seq

Updated Mar 3, 2020
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HectorRDB / NationalAssembly

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A short tutorial to help beginners in biostatistics and genomics understand an usual single-cell RNA-sequencing workflow

tutorial rna-seq politics france scrna-seq-analysis

Updated Jun 22, 2019
HTML

ucdavis-bioinformatics-training / So-you-want-to-do-a-Single-Cell-RNA-seq-experiment

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So you want to do a: Single Cell RNA-seq experiment

seminar scrna scrna-seq-analysis

Updated Nov 6, 2017

llrs / BaseSet_scRNAseq

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Examples of methods for scRNAseq that might benefit from BaseSet

scrna-seq-analysis scrna-imputation-methods

Updated Oct 12, 2019

milescsmith / AutoImpute

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An autoencoder based imputation of the sparse single cell RNA-seq data.

imputation scrna-seq scrna-seq-analysis

Updated Apr 6, 2019
Python

Munfred / wormcells-site

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Gene expression on C. elegans single cells

scrna-seq scrna-seq-data scrna-seq-analysis

Updated Apr 4, 2020
Python

IDG-Kinase / HCA_Kinase_Analysis

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Analysis of HCA Preview Data

bioinformatics scrna-seq-analysis

Updated Sep 27, 2018
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VCCRI / scTalk

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Intercellular communication analysis for scRNA-seq data

scrna-seq scrna-seq-analysis intercellular-communication ligand-receptor

Updated Mar 14, 2020
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dgavr / Single_Cell_Iterative_Pooling

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Iteratively randomly pooling scRNA-seq expressing a given gene from different numbers of cells and running DESeq2 with fdrtools correction to determine how many times which genes come out as enriched with said gene

bootstrap deseq2 scrna-seq iterative-methods fdr scrna-seq-analysis foxd3 neural-crest tsslab