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mirnature
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public |
MiRNAture improves on ideas from MIRfix and integrates it with homology search. miRNAture is specifically designed to identify and annotate metazoan miRNAs in a homology-based setting and is complementary to tools and pipelines that extract miRNA candidates from small RNA-seq data
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2023-06-16 |
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ribolands
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public |
Energy landscapes and folding kinetics of nucleic acids
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2023-06-16 |
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crnsimulator
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public |
Simulate chemical recation networks (CRNs) using ordinary differential equations (ODEs).
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2023-06-16 |
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samap
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public |
The SAMap algorithm
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2023-06-16 |
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vulcan
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public |
vulcan, map long reads and prosperđź––, a long read mapping pipeline that melds minimap2 and NGMLR
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2023-06-16 |
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rnabridge-denovo
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public |
A tool to construct the alignments of entire fragments given the alignments of paired-end reads.
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2023-06-16 |
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jvarkit-wgscoverageplotter
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public |
Whole genome BAM coverage plotter
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2023-06-16 |
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basenji
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public |
Sequential regulatory activity predictions with deep convolutional neural networks.
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2023-06-16 |
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perl-atlas-modules
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public |
A package exporting in-house perl functions and classes used in the data production of EMBL-EBI Expression Atlas data.
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2023-06-16 |
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covid-spike-classification
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public |
Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data.
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2023-06-16 |
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bamtocov
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public |
Extract coverage information from BAM files, supporting stranded and physical coverage and streams.
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2023-06-16 |
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trim_isoseq_polya
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public |
Trims polyA tails from IsoSeq FASTA files
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2023-06-16 |
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trimns_vgp
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public |
TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline.
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2023-06-16 |
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bamsnap
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public |
A converter from .bam to .png for specific genomic region.
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2023-06-16 |
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clusterfunk
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public |
Miscellaneous clustering manipulation tools for phylogenetic trees
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2023-06-16 |
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reportfunk
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public |
Central set of functions generally useful for civet, llama and any report generating tools that may exist in the future
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2023-06-16 |
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fastafunk
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public |
Miscellaneous fasta manipulation tools
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2023-06-16 |
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htseqqc
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public |
HTSeqQC is an automated quality control analysis tool for a single and paired-end high-throughput sequencing data (HTS) generated from Illumina sequencing platforms
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2023-06-16 |
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president
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public |
Calculate pairwise nucleotide identity with respect to a reference sequence.
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2023-06-16 |
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ptools_bin
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public |
Installation for ptools scripts.
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2023-06-16 |
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cov-lineages
|
public |
A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
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2023-06-16 |
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chip-r
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public |
ChIP-R is a method for assessing the reproducibility of replicated ChIP-seq or ATAC-seq experiments.
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2023-06-16 |
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bioconductor-expressionnormalizationworkflow
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public |
Gene Expression Normalization Workflow
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2023-06-16 |
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megatron
|
public |
MEGATRON - MEGA TRajectories of clONes
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2023-06-16 |
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simba
|
public |
SIMBA - SIngle-cell eMBedding Along with features
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2023-06-16 |
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salsa2
|
public |
Salsa is a tool to scaffold long read assemblies with Hi-C.
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2023-06-16 |
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phirbo
|
public |
Predict prokaryotic hosts for phage (meta) genomic sequences
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2023-06-16 |
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primalscheme
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public |
primalscheme is a tool for designing primer panels for multiplex PCR
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2023-06-16 |
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bayesase
|
public |
Bayesian analysis of allele specific expression
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2023-06-16 |
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xtea
|
public |
TE insertion caller for both short and long reads
|
2023-06-16 |
|
run-dbcan
|
public |
Standalone version of dbCAN annotation tool for automated CAZyme annotation
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2023-06-16 |
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pangolearn
|
public |
Store of the trained model for pangolin to access.
|
2023-06-16 |
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spatyper
|
public |
Computational method for finding spa types.
|
2023-06-16 |
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shovill-se
|
public |
An fork of Shovill (microbial assembly pipeline for Illumina paired-end reads) that supports single-end reads.
|
2023-06-16 |
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pulchra
|
public |
A tool for all-atom reconstruction and refinement of reduced protein models
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2023-06-16 |
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datafunk
|
public |
Miscellaneous data manipulation tools for fasta and sam files
|
2023-06-16 |
|
siann
|
public |
SIANN was created to allow creation of local small sets of bacterial/viral genomes to perform strain level differentiation from fastq data
|
2023-06-16 |
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bugseq-porechop
|
public |
Adapter removal and demultiplexing of Oxford Nanopore reads (fork of artic-network/Porechop)
|
2023-06-16 |
|
ribominer
|
public |
A python toolset for mining multi-dimensional features of the translatome with ribosome profiling data
|
2023-06-16 |
|
mitobim
|
public |
mitochondrial baiting and iterative mapping
|
2023-06-16 |
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pargenes
|
public |
A massively parallel tool for model selection and tree inference on thousands of genes
|
2023-06-16 |
|
homopolish
|
public |
Homopolish is a polish tools
|
2023-06-16 |
|
bioprov
|
public |
BioProv - Provenance capture for bioinformatics workflows
|
2023-06-16 |
|
forceatlas2-python
|
public |
Multithreaded Gephi Force Atlas2 Layout algorithm in 2D and 3D, which is used to calculate the pseudo-temporal development trajectory of single-cell data.
|
2023-06-16 |
|
predex
|
public |
Prepare expression data for dgeAnalysis - LUMC.
|
2023-06-16 |
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aodp
|
public |
Cluster oligonucleotide signatures for rapid identification by sequencing
|
2023-06-16 |
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chap
|
public |
CHAP is a tool for the functional annotation of ion channel structures
|
2023-06-16 |
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rfplasmid
|
public |
RFPlasmid predicts plasmid contigs from assemblies using single copy marker genes, plasmid genes, and kmers.
|
2023-06-16 |
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bamaddrg
|
public |
Add read group to BAM files
|
2023-06-16 |
|
ryuto
|
public |
Network-Flow based Transcriptome Reconstruction
|
2023-06-16 |
