Dr. Md. Alamin's repositories
onek1k_phase1
Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types
bpipe
Bpipe - a tool for running and managing bioinformatics pipelines
snakemakeWorkflow
Bioinformatics-pipeline in snakemake.
varCA
Use an ensemble of variant callers to call variants from ATAC-seq data
scPolyA-seq
https://pubmed.ncbi.nlm.nih.gov/36454750/
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.
scConsensus
An approach combining supervised and unsupervised clustering for cell type detection in single-cell RNA-seq data
TENET
TENET is a tool for reconstructing gene regulatory networks from pseudo-time ordered single-cell transcriptomic data.
smartseq2
A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
CLIP-featurevis
code for reproducing some of the diagrams in the paper "Multimodal Neurons in Artificial Neural Networks"
souporcell
Clustering scRNAseq by genotypes
GenABEL
:exclamation: This is a read-only mirror of the CRAN R package repository. GenABEL — genome-wide SNP association analysis. Homepage: http://www.genabel.org, http://forum.genabel.org,<U+000a>http://genabel.r-forge.r-project.org/ Report bugs for this package: http://r-forge.r-project.org/tracker/?group_id=505
DESeq2
Differential gene expression analysis based on the negative binomial distribution
SCINA
SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples
SCSA
SCSA: cell type annotation for single-cell RNA-seq data
vartrix
Single-Cell Genotyping Tool
MAST
Tools and methods for analysis of single cell assay data in R
CellAnnotationTutorial
Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
MathematicaForPrediction
Mathematica implementations of machine learning algorithms used for prediction and personalization.
SINCERA
An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis
VarDict
VarDict
LORSEN
LORSEN R Program
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"