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ucsc-mafranges
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public |
Extract ranges of target (or query) coverage from maf and
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2024-12-12 |
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ucsc-hgloadchain
|
public |
Load a generic Chain file into database
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2024-12-12 |
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ucsc-pslcdnafilter
|
public |
Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
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2024-12-12 |
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ucsc-estorient
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public |
Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped.
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2024-12-12 |
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ucsc-expmatrixtobarchartbed
|
public |
Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
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2024-12-12 |
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fastq-join
|
public |
Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools.
|
2024-12-12 |
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lighter
|
public |
Lighter is a kmer-based error correction method for whole genome sequencing data
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2024-12-12 |
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rapidnj
|
public |
RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.
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2024-12-12 |
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mawk
|
public |
mawk is an interpreter for the AWK Programming Language.
|
2024-12-12 |
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viennarna
|
public |
ViennaRNA package -- RNA secondary structure prediction and comparison
|
2024-12-12 |
|
edena
|
public |
No Summary
|
2024-12-12 |
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fastme
|
public |
a comprehensive, accurate and fast distance-based phylogeny inference program.
|
2024-12-12 |
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perl-bloom-faster
|
public |
Perl extension for the c library libbloom.
|
2024-12-12 |
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emboss
|
public |
The European Molecular Biology Open Software Suite
|
2024-12-12 |
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dnp-fourier
|
public |
Periodogram of dinucleotide frequency pattern
|
2024-12-12 |
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disty
|
public |
Disty McMatrixface - compute a distance matrix from a core genome alignment file.
|
2024-12-12 |
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dextractor
|
public |
Bax File Decoder and Data Compressor
|
2024-12-11 |
|
plek
|
public |
Predictor of long non-coding RNAs and mRNAs based on k-mer scheme.
|
2024-12-11 |
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flash2
|
public |
Merge paired-end reads from fragments that are shorter than twice the read length
|
2024-12-11 |
|
plass
|
public |
Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs
|
2024-12-11 |
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perl-config-any
|
public |
Load configuration from different file formats, transparently
|
2024-12-11 |
|
mdasim
|
public |
This is MDAsim 2+, a tool to simulate whole genome amplification of a DNA sequence with multiple displacement amplification. A citation for this version will be provided when available. MDAsim 2+ extends MDAsim 1.2, so please also always cite: Tagliavi Z, Draghici S. MDAsim: A multiple displacement amplification simulator. 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2012. pp. 1–4. doi:10.1109/BIBM.2012.6392622
|
2024-12-11 |
|
ucsc-hubpubliccheck
|
public |
checks that the labels in hubPublic match what is in the hub labels
|
2024-12-11 |
|
sparseassembler
|
public |
No Summary
|
2024-12-11 |
|
ucsc-gtftogenepred
|
public |
convert a GTF file to a genePred
|
2024-12-11 |
|
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 |
|
perl-tie-hash-indexed
|
public |
Ordered hashes for Perl
|
2024-12-11 |
|
r2r
|
public |
software to speed depiction of aesthetic consensus RNA secondary structures
|
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 |
|
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 |
|
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 |
|
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 |
|
mbuffer
|
public |
mbuffer is a tool for buffering data streams with a large set of unique features
|
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 |
|
rainbow
|
public |
Efficient tool for clustering and assembling short reads, especially for RAD
|
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 |
|
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 |
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ucsc-bedintersect
|
public |
Intersect two bed files
|
2024-12-11 |
