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screpliseq-pipeline

Docker pipeline for analyzing scRepli-seq data

scrna-seq

scrna.seq.course

Analysis of single cell RNA-seq data course

scrna_smart_seq2

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

scrnaseq_clustering_comparison

A study to compare methods for clustering of scRNA-seq data

seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

sgrna

A pipeline for sgRNA design

shinyapp_from_bioxfu

ShinyApp(gominer, heart, ngsminer, overlap, overlap2, sraminer, virus_orf_finder )

single-cell-metabolic-landscape

Pipeline for exploring metebolic heterogeneity at single-cell resolution

single-cell-papers-with-code

Papers with code for single cell related papers

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"

singlecelllineage

Updated scripts and pipelines for processing GESTALT data at single-cell resolution

singlecellrna_melanoma_paper

sirota_lab_covid_drug_repositioning

Drug repositioning pipeline applying a rank-based metric to transcriptomics data to identify potential therapeutics for COVID-19

smaps

A pipeline based on unmapped reads, which combines different tools for extends contigs and closing gaps present in the genomes

smrnaseq

A small-RNA sequencing analysis pipeline

somatic-variant-caller

Somatic variant calling pipeline using Mutect2 adapted from GATK Best Practices

splicelauncher

RNAseq pipeline for alternative splicing junctions

splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

spliz_pipeline

Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis

structural-variations-analysis

Finding structural variations in a genome after comparison with a reference genome.

structurly

Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis

sv-nf

Nextflow workflow for structural variants with graph data

synvisio

SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity detection toolkit.

teachingmaterial

RNA-seq data analysis practical

tempora

Pathway-based trajectory inference method for time-series scRNAseq data

tests-on-eggnog-mapper

tigmint

⛓ Correct misassemblies using linked AND long reads

time2splice

Method to identify temporal and sex-specific alternative splicing from multi-omic data, specifically RNA-seq + (CUT&RUN or ChIP-seq).