Discover soedinglab/CCMgen-scripts Open Source project

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Created over 6 years ago
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Contains plotting scripts, examples, and other small scripts relevant to CCMgen and the corresponding publication.

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

1,391

hh-suite

Remote protein homology detection suite.

535

metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

175

plass

sensitive and precise assembly of short sequencing reads

145

CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.

MMseqs2-App

MMseqs2 app to run on your workstation or servers

Vue

WIsH

Predict prokaryotic host for phage metagenomic sequences

C++

spacedust

Discovery of conserved gene clusters in multiple genomes

uniclust-pipeline

Shell

spacepharer

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

prosstt

PRObabilistic Simulations of ScRNA-seq Tree-like Topologies

Python

CCMgen

HTML

pdbx

pdbx is a parser module in python for structures of the protein data bank in the mmcif format

Python

BaMMmotif

Bayesian Markov Model motif discovery - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

C++

merlot

Reconstruct the lineage topology of a scRNA-seq differentiation dataset.

HTML

kClust

kClust is a fast and sensitive clustering method for the clustering of protein sequences. It is able to cluster large protein databases down to 20-30% sequence identity. kClust generates a clustering where each cluster is represented by its longest sequence (representative sequence).

C++

b-lore

Bayesian multiple logistic regression for GWAS meta-analysis

Python

MMseqs

C++

BaMMmotif2

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

C++

ffindex_soedinglab

tejaas

Tejaas - a tool for discovering trans-eQTLs

bbcontacts

Prediction of beta-strand pairing from direct coupling patterns

Papyrus

hhdatabase_cif70

Scripts to generate the pdb70 database for hh-suite on the basis of pdb's mmcif format

Shell

PEnG-motif

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

C++

transannot

TransAnnot - a fast transcriptome annotation pipeline

BaMM_webserver

Webserver for motif discovery with higher-order Bayesian Markov Models (BaMMs)

HTML

metaG-ECCB18-partII

MMseqs2 tutorial for metagenomics sequence data

TeX

bamm-suite

De-novo motif discovery and optimization

Python

mockinbird

PAR-CLIP data processing pipeline

Python

bipartite_motif_finder

BMF: Bipartite Motif Finder

Python

CoCo

Consensus Correction

C++

MMseqs2-Regression

MMseqs2 Regression Testing

Shell

xxmotif

XXmotif: eXhaustive, weight matriX-based motif discovery in nucleotide sequences

Perl

prosstt-r

An R package with evaluation and visualization functions for the python PROSSTT package

HTML

soedinglab/CCMgen-scripts

soedinglab

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