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ucsc-hgloadbed
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public |
Load a generic bed file into database
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2024-12-11 |
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ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
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2024-12-11 |
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ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
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2024-12-11 |
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rainbow
|
public |
Efficient tool for clustering and assembling short reads, especially for RAD
|
2024-12-11 |
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ucsc-liftup
|
public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
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2024-12-11 |
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treebest
|
public |
TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline.
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2024-12-11 |
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gmtk
|
public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
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2024-12-11 |
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r-epic
|
public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
|
2024-12-11 |
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ucsc-bedintersect
|
public |
Intersect two bed files
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2024-12-11 |
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genesplicer
|
public |
No Summary
|
2024-12-11 |
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ucsc-genepredsinglecover
|
public |
create single-coverage genePred files
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2024-12-11 |
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ucsc-parasync
|
public |
uses paraFetch to recursively mirror url to given path
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2024-12-11 |
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ncrf
|
public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
|
2024-12-11 |
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gnu-wget
|
public |
No Summary
|
2024-12-11 |
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ucsc-validatefiles
|
public |
Validates the format of different genomic files.
|
2024-12-11 |
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r-gwpcr
|
public |
Implements the necessary distributions and parameter estimation procedures for a model of amplification and high-troughput sequencing. The model is based on a mechanistic model of PCR amplification as a Galton-Watson branching process, and on Poissonan sampling to model high-throughput sequencing.
|
2024-12-11 |
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msisensor
|
public |
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
|
2024-12-11 |
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extract-sv-reads
|
public |
Tool for extracting splitter or discordant reads from a BAM or CRAM file.
|
2024-12-11 |
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plink
|
public |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
|
2024-12-11 |
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prophasm
|
public |
ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
|
2024-12-11 |
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extract_fullseq
|
public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-12-11 |
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ucsc-lavtopsl
|
public |
Convert blastz lav to psl format
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2024-12-11 |
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filtlong
|
public |
Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
|
2024-12-11 |
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mgs-canopy
|
public |
No Summary
|
2024-12-11 |
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ucsc-bigwigtobedgraph
|
public |
Convert from bigWig to bedGraph format.
|
2024-12-11 |
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htsbox
|
public |
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files.
|
2024-12-11 |
|
ir
|
public |
Program for Calculating the Repetitiveness of DNA Sequences
|
2024-12-11 |
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ucsc-pslliftsubrangeblat
|
public |
lift PSLs from blat subrange alignments
|
2024-12-11 |
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ococo
|
public |
Ococo, the first online consensus caller.
|
2024-12-11 |
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potrace
|
public |
A tool for tracing a bitmap, which means, transforming a bitmap into a smooth, scalable image
|
2024-12-11 |
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seqyclean
|
public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
|
2024-12-11 |
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prophex
|
public |
The ProPhex k-mer index.
|
2024-12-11 |
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ucsc-para
|
public |
version 12.18
|
2024-12-11 |
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ucsc-featurebits
|
public |
Correlate tables via bitmap projections.
|
2024-12-11 |
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biolite-tools
|
public |
C++ tools for biolite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
|
2024-12-11 |
|
codonw
|
public |
CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
|
2024-12-11 |
|
lrzip
|
public |
Long Range ZIP or Lzma RZIP. This is a compression program optimised for large files. The larger the file and the more memory you have, the better the compression advantage this will provide, especially once the files are larger than 100MB. The advantage can be chosen to be either size (much smaller than bzip2) or speed (much faster than bzip2).
|
2024-12-11 |
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ucsc-chainnet
|
public |
Make alignment nets out of chains
|
2024-12-11 |
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thermorawfileparser
|
public |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono
|
2024-12-11 |
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collect_mgf
|
public |
Collects MGF files and dd_results from an XMass setup_QDD.tcl experiment to a single MGF file.
|
2024-12-11 |
|
yaha
|
public |
No Summary
|
2024-12-11 |
|
metacluster
|
public |
No Summary
|
2024-12-11 |
|
ray
|
public |
No Summary
|
2024-12-11 |
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ucsc-genepredtofakepsl
|
public |
Create a psl of fake-mRNA aligned to gene-preds from a file or table.
|
2024-12-11 |
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ucsc-rasqlquery
|
public |
Do a SQL-like query on a RA file.
|
2024-12-11 |
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gotohscan
|
public |
a search tool that finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, ..) by computing all semi-global alignments.
|
2024-12-11 |
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ucsc-gff3togenepred
|
public |
convert a GFF3 file to a genePred file
|
2024-12-11 |
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lightstringgraph
|
public |
LightStringGraphs (LSG) is an external memory string graph construction tool.
|
2024-12-11 |
|
rust-overlaps
|
public |
A fast and secure command line utilility for enumerating all suffix-prefix
overlaps within a set of sequences, satisfying a user-specified minimal
overlap length and maximal error rate.
|
2024-12-11 |
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ucsc-sqltoxml
|
public |
dump out all or part of a relational database to XML, guided
|
2024-12-11 |
