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ucsc-parasol
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public |
Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users.
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2024-12-13 |
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ucsc-twobitmask
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public |
apply masking to a .2bit file, creating a new .2bit file
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2024-12-13 |
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ucsc-facount
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public |
count base statistics and CpGs in FA files.
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2024-12-13 |
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bcov
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public |
BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.
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2024-12-13 |
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ucsc-mafgene
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public |
output protein alignments using maf and genePred
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2024-12-13 |
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ntcard
|
public |
Estimating k-mer coverage histogram of genomics data
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2024-12-13 |
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cgmlst-dists
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public |
Convert cgMLST table to distance matrix
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2024-12-13 |
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desalt
|
public |
De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
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2024-12-13 |
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ucsc-chaintopsl
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public |
Convert chain file to psl format
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2024-12-13 |
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perl-unicode-utf8
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public |
Encoding and decoding of UTF-8 encoding form
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2024-12-13 |
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lambda
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public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
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2024-12-13 |
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ucsc-bedcommonregions
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public |
Create a bed file (just bed3) that contains the regions common to all inputs.
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2024-12-13 |
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nxtrim
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public |
Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.
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2024-12-13 |
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dnp-mapping
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public |
Mapping of a nuclesome position in sequence by pattern
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2024-12-13 |
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fasta_windows
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public |
Generate fast sequence statistics in windows for each record in a fasta file.
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2024-12-13 |
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minigraph
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public |
Proof-of-concept seq-to-graph mapper and graph generator
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2024-12-13 |
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ucsc-genepredcheck
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public |
validate genePred files or tables
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2024-12-13 |
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ucsc-paranode
|
public |
version 12.18
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2024-12-13 |
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kssd
|
public |
K-mer substring space decomposition
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2024-12-13 |
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kakscalculator2
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public |
KaKs_Calculator2.0 calculates Ka and Ks.
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2024-12-13 |
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r-singlecellnet
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public |
SingleCellNet enables the classifcation of single cell RNA-Seq data across
species and platforms.
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2024-12-13 |
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fpa
|
public |
Filter Pairwise Alignment filter long read mapping information to save disk space
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2024-12-13 |
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pftools
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public |
A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation.
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2024-12-13 |
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msamtools
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public |
microbiome-related extension to samtools
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2024-12-13 |
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mason
|
public |
Mason is a collection of tools for the simulation of biological sequences.
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2024-12-13 |
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perl-statistics-caseresampling
|
public |
Efficient resampling and calculation of medians with confidence intervals
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2024-12-13 |
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ucsc-maftobigmaf
|
public |
Put ucsc standard maf file into bigMaf format
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2024-12-13 |
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bxtools
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public |
Tools for analyzing 10X Genomics data
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2024-12-13 |
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stereogene
|
public |
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
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2024-12-13 |
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r-minionqc
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public |
Quality control for MinION sequencing data
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2024-12-13 |
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plink2
|
public |
Whole genome association analysis toolset
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2024-12-13 |
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ucsc-axttopsl
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public |
Convert axt to psl format
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2024-12-13 |
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srnamapper
|
public |
Mapping small RNA data to a genome.
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2024-12-13 |
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distle
|
public |
Fast distance matrix calculations on fasta and cgmlst files
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2024-12-13 |
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ucsc-fanoise
|
public |
Add noise to .fa file
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2024-12-13 |
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hi-corrector
|
public |
Remove biases from chromatin contact matrices generated by genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC
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2024-12-13 |
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jarvis
|
public |
Efficient lossless compression of genomic sequences
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2024-12-13 |
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chromap
|
public |
Fast alignment and preprocessing of chromatin profiles
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2024-12-13 |
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ucsc-htmlcheck
|
public |
Do a little reading and verification of html file
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2024-12-13 |
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simba_pbg
|
public |
A customized PyTorch-BigGraph (PBG) package for `simba`
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2024-12-13 |
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comparems2
|
public |
A simple tool developed to compare, globally, all MS/MS spectra between two datasets (in Mascot Generic Format or MGF).
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2024-12-13 |
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migrate-n
|
public |
Population Genetics - Panmixia and Migration detection
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2024-12-13 |
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strike
|
public |
A program to evaluate protein multiple sequence alignments using a single protein structure.
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2024-12-13 |
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fastspar
|
public |
Rapid and scalable correlation estimation for compositional data
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2024-12-13 |
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ucsc-texthistogram
|
public |
Make a histogram in ascii
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2024-12-13 |
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simbac
|
public |
SimBac simulates bacterial genomes with the clonal genealogy under a coalescent model with recombination.
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2024-12-13 |
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dehomopolymerate
|
public |
Collapse homopolymer runs in FASTQ files
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2024-12-13 |
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hcluster_sg
|
public |
A tool for hierarchically clustering on a sparse graph
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2024-12-13 |
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ucsc-bigwigtowig
|
public |
Convert bigWig to wig. This will keep more of the same structure of the
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2024-12-13 |
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subread
|
public |
High-performance read alignment, quantification, and mutation discovery.
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2024-12-13 |
