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ucsc-maffilter
|
public |
Filter out maf files. Output goes to standard out
|
2024-12-13 |
|
r-annotables
|
public |
Provides tables for converting and annotating Ensembl Gene IDs.
|
2024-12-13 |
|
ucsc-pslrecalcmatch
|
public |
Recalculate match,mismatch,repMatch columns in psl file.
|
2024-12-13 |
|
ucsc-axtchain
|
public |
Chain together axt alignments.
|
2024-12-13 |
|
ucsc-parasol
|
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.
|
2024-12-13 |
|
ucsc-twobitmask
|
public |
apply masking to a .2bit file, creating a new .2bit file
|
2024-12-13 |
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ucsc-facount
|
public |
count base statistics and CpGs in FA files.
|
2024-12-13 |
|
bcov
|
public |
BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.
|
2024-12-13 |
|
ucsc-mafgene
|
public |
output protein alignments using maf and genePred
|
2024-12-13 |
|
ntcard
|
public |
Estimating k-mer coverage histogram of genomics data
|
2024-12-13 |
|
ucsc-chaintopsl
|
public |
Convert chain file to psl format
|
2024-12-13 |
|
perl-unicode-utf8
|
public |
Encoding and decoding of UTF-8 encoding form
|
2024-12-13 |
|
lambda
|
public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
|
2024-12-13 |
|
ucsc-bedcommonregions
|
public |
Create a bed file (just bed3) that contains the regions common to all inputs.
|
2024-12-13 |
|
ucsc-genepredcheck
|
public |
validate genePred files or tables
|
2024-12-13 |
|
ucsc-paranode
|
public |
version 12.18
|
2024-12-13 |
|
fpa
|
public |
Filter Pairwise Alignment filter long read mapping information to save disk space
|
2024-12-13 |
|
mason
|
public |
Mason is a collection of tools for the simulation of biological sequences.
|
2024-12-13 |
|
ucsc-maftobigmaf
|
public |
Put ucsc standard maf file into bigMaf format
|
2024-12-13 |
|
bxtools
|
public |
Tools for analyzing 10X Genomics data
|
2024-12-13 |
|
stereogene
|
public |
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
|
2024-12-13 |
|
plink2
|
public |
Whole genome association analysis toolset
|
2024-12-13 |
|
ucsc-axttopsl
|
public |
Convert axt to psl format
|
2024-12-13 |
|
ucsc-fanoise
|
public |
Add noise to .fa file
|
2024-12-13 |
|
ucsc-htmlcheck
|
public |
Do a little reading and verification of html file
|
2024-12-13 |
|
comparems2
|
public |
A simple tool developed to compare, globally, all MS/MS spectra between two datasets (in Mascot Generic Format or MGF).
|
2024-12-13 |
|
migrate-n
|
public |
Population Genetics - Panmixia and Migration detection
|
2024-12-13 |
|
strike
|
public |
A program to evaluate protein multiple sequence alignments using a single protein structure.
|
2024-12-13 |
|
fastspar
|
public |
Rapid and scalable correlation estimation for compositional data
|
2024-12-13 |
|
ucsc-texthistogram
|
public |
Make a histogram in ascii
|
2024-12-13 |
|
hcluster_sg
|
public |
A tool for hierarchically clustering on a sparse graph
|
2024-12-13 |
|
ucsc-bigwigtowig
|
public |
Convert bigWig to wig. This will keep more of the same structure of the
|
2024-12-13 |
|
subread
|
public |
High-performance read alignment, quantification, and mutation discovery.
|
2024-12-13 |
|
ucsc-bigwigcluster
|
public |
Cluster bigWigs using a hacTree
|
2024-12-13 |
|
ucsc-bigwigaverageoverbed
|
public |
Compute average score of big wig over each bed, which may have introns.
|
2024-12-13 |
|
age-metasv
|
public |
optimal alignment of sequences with structural variants (SVs), modifiied for MetaSV integration
|
2024-12-13 |
|
raxml
|
public |
Phylogenetics - Randomized Axelerated Maximum Likelihood.
|
2024-12-13 |
|
ucsc-paranodestatus
|
public |
version 12.18
|
2024-12-13 |
|
weeder
|
public |
No Summary
|
2024-12-13 |
|
pullseq
|
public |
No Summary
|
2024-12-13 |
|
ucsc-pslpartition
|
public |
split PSL files into non-overlapping sets
|
2024-12-13 |
|
snap-aligner
|
public |
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
|
2024-12-13 |
|
perl-dbd-pg
|
public |
DBI PostgreSQL interface
|
2024-12-13 |
|
bmfilter
|
public |
bmfilter is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-12-13 |
|
ucsc-lavtoaxt
|
public |
Convert blastz lav file to an axt file (which includes sequence)
|
2024-12-13 |
|
bedtools
|
public |
A powerful toolset for genome arithmetic
|
2024-12-13 |
|
ucsc-ixixx
|
public |
Create indices for simple line-oriented file of format
|
2024-12-13 |
|
perl-io-compress
|
public |
IO Interface to compressed data files/buffers
|
2024-12-13 |
|
ucsc-newpythonprog
|
public |
Make a skeleton for a new python program
|
2024-12-13 |
|
flexbar
|
public |
Flexible barcode and adapter removal
|
2024-12-13 |
