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3dmax

A maximum likelihood method for reconstructing 3D chromosome structure from chromosomal contact data

ampssembler

This project contains scripts,source codes, documents, etc. associated with the AMPssembler Project.

apa

apa: research platform for the study of alternative polyadenylation, apaexpress.org

arcplot

Code for plotting arcs

badread

a long read simulator that can imitate many types of read problems

bam2m5

convert bam file to Pacbio m5 format

barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba

basset

Convolutional neural network analysis for predicting DNA sequence activity.

beforephylo

Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction

beyond_memory_v2

biers

Basic Inference Engine for RNA Structure

binarydist

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

bioblender21

Blender plugin to process biological data and molecular work.

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bowtie2

A fast and sensitive gapped read aligner

bumhmm

BUM-HMM is a statistical modelling pipeline for interpreting high-throughput RNA structure probing data.

canu

A single molecule sequence assembler for genomes large and small.

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

cgat-apps

cgat-apps repository

codequery

A code-understanding, code-browsing or code-search tool. This is a tool to index, then query or search C, C++, Java, Python, Ruby, Go and Javascript source code. It builds upon the databases of cscope and ctags, and provides a nice GUI tool.

codon_tasep

simulate TASEP model with codon-specific elongation rates

cofold

An RNA secondary structure prediction method that takes co-transcriptional folding into account

cogent

Coding Genome Reconstruction using Iso-Seq data

collepardolab_chromatin_model

Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".

comrades

A program for folding RNA using constraints from proximity ligation experiments

cotrans_shape-seq_tools

Tools for Processing Cotranscriptional SHAPE-Seq Datasets

dart

DNA, Amino Acid and RNA Tests

dms-map-seq-code