zhangyuqing/ComBat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

Language: R - Size: 597 MB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 177 - Forks: 38

thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

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MartinLoza/Canek

Unbiased integration of single cell transcriptomes.

Language: R - Size: 38.4 MB - Last synced at: 20 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

ylaboratory/ALPINE

ALPINE is a semi-supervised non-negative matrix factorization (NMF) framework designed to effectively distinguish between multiple phenotypic conditions based on shared biological factors, while also providing direct interpretability of condition-associated genes. The preprint is available on bioRxiv.

Language: Python - Size: 1.03 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 2 - Forks: 1

Freddsle/fedRBE

decentralized privacy-preserving federated batch effect correction tool for omics data based on limma

Language: Jupyter Notebook - Size: 4.06 GB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

jumphone/BEER

BEER: Batch EffEct Remover for single-cell data

Language: R - Size: 60.1 MB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 24 - Forks: 9

chriscainx/mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Language: Python - Size: 1.05 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 73 - Forks: 32

theislab/kBET

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

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uds-helms/BEclear

Correction of batch effects in DNA methylation data

Language: R - Size: 1.07 MB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

stopsack/batchtma

batchtma: R package to adjust for batch effects, for example between tissue microarrays

Language: R - Size: 11.3 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

symbioticMe/proBatch

Tools for Batch Effects Diagnostics and Correction

Language: R - Size: 4.73 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 6

symbioticMe/batch_effects_workflow_code

Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics

Language: R - Size: 12.2 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 2

fedeago/NewWave

NewWave

Language: R - Size: 6.32 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 2

pavlin-policar/ALRA

Imputation method for scRNA-seq based on low-rank approximation

Language: Python - Size: 2.69 MB - Last synced at: 20 days ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 1

nkimoto/sc_batch_remove

Wrapper of batch removal method for scRNA-seq

Language: R - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 1

mbongaerts/Metchalizer

Language: Jupyter Notebook - Size: 156 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

SLINGhub/StratiRandom

R script and Shiny app to perform stratified randomisation

Language: R - Size: 95.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

tengfei-emory/scBatch

Batch Effect Correction of RNA-seq Data through Sample Distance Matrix Adjustment

Language: R - Size: 1.85 MB - Last synced at: 19 days ago - Pushed at: almost 4 years ago - Stars: 17 - Forks: 9

biolab/tsne-embedding

Embedding to Reference t-SNE Space Addresses Batch Effects in Single-Cell Classification

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tengfei-emory/QuantNorm

Mitigating the adverse impact of batch effects in sample pattern detection

Language: R - Size: 5.98 MB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 9 - Forks: 2

KChen-lab/bcd

Visualization and analysis of single-cell RNA-seq data by alternative clustering

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uds-helms/BEclear-CL

Correction of batch effects with BEclear as a command line tool

Language: R - Size: 802 KB - Last synced at: 7 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

genepattern/ComBat_Seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq

Language: R - Size: 57 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

SkadiEye/RZiMM

RZiMM: A Regularized Zero-inflated Mixture Model for scRNA-seq Data

Language: R - Size: 5.18 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

neuroquant/fmri-site-effects

Uses regression and factor model approach to correct for site effects in fMRI volumes

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mRcSchwering/Lattirl

Package for analyzing batch effects in single cell RNA sequencing (scRNA-seq) analysis and predicting their impact on downstream analysis.

Language: R - Size: 92 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

mRcSchwering/scRNAseq_batchEffects

Analyzing batch effects in single cell RNA sequencing (scRNA-seq) analysis and predicting their impact on downstream analysis.

Language: R - Size: 14.1 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

HaidYi/DASC

Detecting hidden batch factors through data adaptive adjustment for biological effects

Language: R - Size: 1.58 MB - Last synced at: about 1 month ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 3

neuroquant/tutorial-prni-2017

This repository contains iPython notebooks that run on the octave kernel to accompany tutorial and slides presented at PRNI

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