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knn-smoothing

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

learn-bioinformatics

List of resources for learning bioinformatics, from beginner to advanced

liger

R package for integrating and analyzing multiple single-cell datasets

lineagepulse

Differential expression analysis for single-cell RNA-seq data

mutations

calling variants from RNA-Seq data

myscrna-seq

myshiny

ngs-pipeline

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

parainflammation

pipeline-exome

whole exome sequencing analysis pipeline

plate_scatac-seq

A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method

proatac

Preprocessing pipeline for (sc)ATAC data

python-rosalind

This repository contains my Rosalind answers for all of the following questions (all have been tested and work): Installing Python Counting DNA Nucleotides Strings and Lists Working with Files Dictionaries Transcribing DNA into RNA Translating RNA into Protein Find the Reverse Complement of a String Inferring mRNA from Protein Transitions and Transversions Generate the k-mer Composition of a String Reconstruct a String from its Genome Path Constructing a De Bruijn Graph Open Reading Frames Counting Point Mutations Finding a Motif in DNA Edit Distance Edit Distance Alignment Finding a Shared Motif Creating a Distance Matrix Construct the Suffix Array of a String Reconstruct a String from its Burrows-Wheeler Transform Enumerating Gene Orders Enumerating Oriented Gene Orderings RNA Splicing Finding a Spliced Motif Mendel's First Law Compute the Probability of a Hidden Path Compute the Probability of an Outcome Given a Hidden Path Implement the Viterbi Algorithm Conditions and Loops Mortal Fibonacci Rabbits Finding a Protein Motif Error Correction in Reads Global Alignment with Scoring Matrix Local Alignment with Scoring Matrix

reductionwrappers

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

river

R package for RIVER (RNA-Informed Variant Effect on Regulation)

rnamosaicmutationfinder

Somatic variant calling tools for RNAseq data

rnaseq-analysis

Automatic analysis of RNAseq reads: Gene counting + SNP calling. Unix slurm environment

rnaseq.mutation

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rnaseqsnp

scasat

Scasat is a single cell ATAC-seq preprocessing and analysis pipeline

scatac

Multiplex single-cell ATAC-seq analysis pipeline (Ren Lab)

scatac-benchmarking

Benchmarking computational single cell ATAC-seq methods

scatacseq-analysis-notes

my notes for scATACseq analysis

scatactools

R, python, unix tools for 10x scATACseq data

scatacutils

R/Bioconductor package for working with 10x scATACseq data

sccloudpy

scplot

Plotting tools for scCloud

scrna

Use svm to infer stem cell

scrna-1

single cell RNA-seq analysis scripts.