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art_marzooplclk

Accompanying repository for the publication "RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton"

b-lore

Bayesian multiple logistic regression for GWAS meta-analysis

bamm-benchmark

Scripts and data for generating the benchmarks in the W Ge, et al. paper.

bamm-suite

De-novo motif discovery and optimization

bamm_webserver

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

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.

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.

bbcontacts

Prediction of beta-strand pairing from direct coupling patterns

bipartite_motif_finder

BMF: Bipartite Motif Finder

bmf-paper

Notebooks to reproduce the analyses in BMF manuscript

bmf-webserver

Web server for Bipartite Motif Finder (BMF)

ccmgen

ccmgen-scripts

Contains plotting scripts, examples, and other small scripts relevant to CCMgen and the corresponding publication.

ccmpred

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

coco

Consensus Correction

contactpred-felsenstein

Felsenstein implementation for phylogeny correction

cooperative_rbp

csblast

Context-specific mutation probabilities for protein sequencing searching.

csgraph_mod

Modification of the scipy csgraph class to allow tracking of the visited nodes

degradation_scripts

data analysis scripts for degradation pathway story

ffindex_soedinglab

gxpred

Development branch of GxPRED

hh-suite

Remote protein homology detection suite.

hhdatabase_cif70

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

hhdatabase_pfam

Scripts to generate the pfam database for hh-suite

hhdatabase_scop

Build scripts for the scop databases for hh-suite

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).

merlot

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

merlot-scripts

Benchmark and plotting scripts for the MERLoT paper

metaeuk

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