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ucsc-gtftogenepred
|
public |
convert a GTF file to a genePred
|
2024-12-11 |
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mageck
|
public |
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
|
2024-12-11 |
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perl-tie-hash-indexed
|
public |
Ordered hashes for Perl
|
2024-12-11 |
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r2r
|
public |
software to speed depiction of aesthetic consensus RNA secondary structures
|
2024-12-11 |
|
rock
|
public |
ROCK - Reducing Over-Covering K-mers
|
2024-12-11 |
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bicseq2-norm
|
public |
BICseq2-norm is for normalizing potential biases in the sequencing data.
|
2024-12-11 |
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rtk2
|
public |
rtk2 - a CLI rarefaction toolkit for OTU tables
|
2024-12-11 |
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finemap
|
public |
Program for identifying causal SNPs and their effect sizes and heritability contributions
|
2024-12-11 |
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chromimpute
|
public |
ChromImpute is software for large-scale systematic epigenome imputation.
|
2024-12-11 |
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rnahybrid
|
public |
RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA.
|
2024-12-11 |
|
r-firebrowser
|
public |
An R client for broads firehose pipeline, providing TCGA data sets.
|
2024-12-11 |
|
r-ddir
|
public |
An R package to access to Omics Discovery Index API
|
2024-12-11 |
|
heinz
|
public |
The algorithm for identification of the optimal scoring subnetwork.
|
2024-12-11 |
|
perl-filesys-df
|
public |
Perl extension for filesystem disk space information.
|
2024-12-11 |
|
cryfa
|
public |
A secure encryption tool for genomic data
|
2024-12-11 |
|
famseq
|
public |
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013 Mar 5;110(10):3985-90
|
2024-12-11 |
|
gemf_favites
|
public |
User-friendly epidemic simulations
|
2024-12-11 |
|
radtk
|
public |
A collection of tools for working with RAD files.
|
2024-12-11 |
|
fineradstructure
|
public |
Inference of population structure from RAD datasets
|
2024-12-11 |
|
rnaz
|
public |
predicting structural noncoding RNAs
|
2024-12-11 |
|
ucsc-genepredtobiggenepred
|
public |
converts genePred or genePredExt to bigGenePred input (bed format with extra fields)
|
2024-12-11 |
|
pyrodigal
|
public |
Python bindings to Prodigal, an ORF finder for microbial sequences.
|
2024-12-11 |
|
hardklor
|
public |
Analyze mass spectra
|
2024-12-11 |
|
ucsc-checkcoveragegaps
|
public |
Check for biggest gap in coverage for a list of tracks.
|
2024-12-11 |
|
debwt
|
public |
A efficient method to construct BWT index of a given DNA sequence, especially
useful for gigantic and high similar genome.
DeBWT has good scalability to construct BWT in parallel computing.
It is well-suited to run on multiple core servers or clusters to
construct the BWT of large collections of genome sequences.
|
2024-12-11 |
|
verifybamid
|
public |
No Summary
|
2024-12-11 |
|
ucsc-bamtopsl
|
public |
Convert a bam file to a psl and optionally also a fasta file that contains the reads.
|
2024-12-11 |
|
mentalist
|
public |
The MLST pipeline developed by the PathOGiST research group.
|
2024-12-11 |
|
comet-ms
|
public |
Comet is a command line tool that does MS/MS database search.
|
2024-12-11 |
|
ucsc-hgloadbed
|
public |
Load a generic bed file into database
|
2024-12-11 |
|
ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
|
2024-12-11 |
|
ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
|
2024-12-11 |
|
mutscan
|
public |
Detect and visualize target mutations by scanning FastQ files directly
|
2024-12-11 |
|
rainbow
|
public |
Efficient tool for clustering and assembling short reads, especially for RAD
|
2024-12-11 |
|
rabbitqcplus
|
public |
RabbitQCPlus is an efficient quality control tool for sequencing data
|
2024-12-11 |
|
ucsc-liftup
|
public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
|
2024-12-11 |
|
treebest
|
public |
TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara pipeline.
|
2024-12-11 |
|
irf
|
public |
Inverted Repeats Finder is a program that detects approximate inverted repeats.
|
2024-12-11 |
|
gmtk
|
public |
A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)
|
2024-12-11 |
|
r-epic
|
public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
|
2024-12-11 |
|
ucsc-bedintersect
|
public |
Intersect two bed files
|
2024-12-11 |
|
genesplicer
|
public |
No Summary
|
2024-12-11 |
|
ucsc-genepredsinglecover
|
public |
create single-coverage genePred files
|
2024-12-11 |
|
ucsc-parasync
|
public |
uses paraFetch to recursively mirror url to given path
|
2024-12-11 |
|
ncrf
|
public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
|
2024-12-11 |
|
tepeaks
|
public |
Package for including repetitive regions in peak calling from ChIP-seq datasets.
|
2024-12-11 |
|
gnu-wget
|
public |
No Summary
|
2024-12-11 |
|
ucsc-validatefiles
|
public |
Validates the format of different genomic files.
|
2024-12-11 |
|
strainseeker
|
public |
A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
|
2024-12-11 |
|
pcaone
|
public |
PCAone - Principal Component Analysis All in One
|
2024-12-11 |
