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clam

CLIP-seq Analysis of Multi-mapped reads

clear

direct comparison of circular and linear RNA expression

clinker

Gene cluster comparison figure generator

clipseqtools

A suite for the analysis of CLIP-Seq datasets.

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

common-workflow-language

Repository for the CWL standards. Use https://www.biostars.org/t/cwl/ for support 😊

course_rna-seq2018

covcalc

Coverage / read count calculator for sequencing experiments

cv

Dr Manoj K Valluru - Curriculum vitae

cwl-website

www.commonwl.org

dabest-python

Data Analysis with Bootstrapped ESTimation

darts

Deep-learning Augmented RNA-seq analysis of Transcript Splicing

decode

This is the official implementation of our preprint "Deep learning enables fast and dense single-molecule localization with high accuracy"

deeplearning-digital-pathology

Full package for applying deep learning to virtual slides.

deeppath

Classification of Lung cancer slide images using deep-learning

deepvariant

Google's DeepVariant variant caller as a Nextflow pipeline

design

OME Design proposals

dge_workshop

dnapi

De novo adapter prediction algorithm for small RNA sequencing data

ec-dtu-paper

Fast and accurate differential transcript usage by testing equivalence class counts

emirna

eMIRNA pipeline for homology-based and de novo miRNA discovery and annotation

encode_mirna_pipeline

enhancedvolcano

Publication-ready volcano plots with enhanced colouring and labeling

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

eve

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

excerpt

Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets

fastq-pair

Match up paired end fastq files quickly and efficiently.

forestqc

Random forest classifier for variants quality control

galig

A graph aligner

gatk3-4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools