dieterich-lab/single-cell-nanopore

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Created about 5 years ago
Updated almost 3 years ago

dieterich-lab/single-cell-nanopore

dieterich-lab

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Workflow for Nanopore Sequencing of 10x single cell libraries

DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

circtools

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

JACUSA2

New version of JACUSA -> 2.0

AppleDashboard

Dashboard for analysis of Apple Watch data with interactive graphics.

JACUSA

JAVA framework for accurate SNV assessment

CircTest

CircRNA testing and ploting R package

CellPlot

R package for the integrated visualisation of functional enrichment and expression data.

Baltica

Baltica: integrated differential junction usage

rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

ScNaST

ScNaST (Single-cell Nanopore Spatial Transcriptomics)

Jupyter Notebook

medex

Intuitive Graphical User Interface for Medical Data Exploration

JACUSA2helper

Auxiliary R package for assessment of JACUSA2 results

dorina

doRiNa - database of posttranscriptional regulatory elements

Jupyter Notebook

cyntenator

Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes.

magnetiqueCode2022

Source code repository for informatics for life SP1

Jupyter Notebook

ASyH

The Anonymous Synthesizer for Health Data

clinical_deid

De-Identification of Clinical Admission Notes using BiLSTM and Embedded Languages Models (ELMo) as Word Representation

FUCHS

FUCHS - FUll circle CHaracterization from rna-Seq

mAFiA

AnonymizeAndSynthesize

Code used to produce the results presented in the publication "Anonymize or Synthesize? - Privacy-Preserving Methods for Heart Failure Score Analytics"

tribe-workflow

A workflow for TRIBE data based on JACUSA

QutRNA

slurm-tools

A collection of helper scripts for everyday use of SLURM

pulseR

HiGHmedUCCScores

Scoring functions of the HiGHmed use case Cardiology

3PD

Repository of the 3PD tool: Rapid design of optimal primers for chromosome conformation capture assays

bioinfo-scripts

Assorted scripts in Perl, Bash, R and whatsoever directly from a bioinformaticians scripts/ folder

PETGUI

We present PETGUI: A user-friendly interface for training and testing a language model using Pattern-Exploiting Training (PET).

MiMB_JACUSA2_chapter

JACUSA2 - A framework for the mapping of RNA modifications

primex

bareos-scripts

LINDA

rajman_et_al

Supplementary software and custom scripts for Rajman et al.

nmdtxdb

Shiny application and code for the database for NMD targets