AhmedArslan

HbCGM_paper

codes used in HbCGM_paper

MRsimplify

TwosampleMR and MultivariableMR perform with simple commands without prior knowledge or having to go through lengthy boring protocols

AGAT

Another Gtf/Gff Analysis Toolkit

AnchorWave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

awesome-vdj

📚 Tools and databases for analyzing HLA and VDJ genes.

bamnostic

a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool

CartoGRAPHs

ccsmeth

Detecting DNA methylation from PacBio CCS reads

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

DeepSVP

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity

doppelganger

Target site duplication assessment from alignment file and genomic location of insertion sites.

gos

A declarative library for Python designed to create interactive multi-scale visualizations of genomics and epigenomics data.

GREEN-VARAN

Annotate non-coding regulatory vars using our GREEN-DB, prediction scores, conservation and pop AF

GWASimplify

help in performing all gwas steps from QC to functional assessments for case-control analyses.

HiFiCNV

Copy number variant caller and depth visualization utility for PacBio HiFi reads

imavirus

lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

lrRNAseqVariantCalling

Codes for the Iso-Seq variant-calling paper

MetBrewer

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

ml-genomics-resources

Machine Learning for Genomics and Therapeutics Resources (Cell Patterns)

nanotei

A pipeline for detection of non-reference transposon insertions using Nanopore data

PALMER

Pre-mAsking Long reads for Mobile Element inseRtion

pepper

PEPPER-Margin-DeepVariant

plotsr

Tool to plot synteny and structural rearrangements between genomes

RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

saturation

:sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

smashpp

Find and visualize rearrangements in DNA sequences

Stata-schemes

Here you will find various ready-to-use Stata schemes.

swan_vis

A Python library to visualize and analyze long-read transcriptomes