|
epa-ng
|
public |
Massively parallel phylogenetic placement of genetic sequences
|
2024-12-13 |
|
btrim
|
public |
This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
|
2024-12-13 |
|
prosampler
|
public |
An ultra-fast motif finding program in large ChIP-seq datasets.
|
2024-12-13 |
|
ucsc-genepredtomafframes
|
public |
create mafFrames tables from a genePreds
|
2024-12-13 |
|
ncls
|
public |
Fast overlap datastructure.
|
2024-12-13 |
|
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 |
|
centrifuge-core
|
public |
Classifier for metagenomic sequences. Does not include evaluation scripts
|
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 |
|
tttrlib
|
public |
A file format agnostic library for time-resolved imaging and spectroscopic data.
|
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 |
|
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 |
|
cgmlst-dists
|
public |
Convert cgMLST table to distance matrix
|
2024-12-13 |
|
desalt
|
public |
De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
|
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 |
|
nxtrim
|
public |
Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.
|
2024-12-13 |
|
dnp-mapping
|
public |
Mapping of a nuclesome position in sequence by pattern
|
2024-12-13 |
|
fasta_windows
|
public |
Generate fast sequence statistics in windows for each record in a fasta file.
|
2024-12-13 |
|
minigraph
|
public |
Proof-of-concept seq-to-graph mapper and graph generator
|
2024-12-13 |
|
ucsc-genepredcheck
|
public |
validate genePred files or tables
|
2024-12-13 |
|
ucsc-paranode
|
public |
version 12.18
|
2024-12-13 |
|
kssd
|
public |
K-mer substring space decomposition
|
2024-12-13 |
|
r-singlecellnet
|
public |
SingleCellNet enables the classifcation of single cell RNA-Seq data across
species and platforms.
|
2024-12-13 |
|
fpa
|
public |
Filter Pairwise Alignment filter long read mapping information to save disk space
|
2024-12-13 |
|
pftools
|
public |
A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation.
|
2024-12-13 |
|
msamtools
|
public |
microbiome-related extension to samtools
|
2024-12-13 |
|
mason
|
public |
Mason is a collection of tools for the simulation of biological sequences.
|
2024-12-13 |
|
perl-statistics-caseresampling
|
public |
Efficient resampling and calculation of medians with confidence intervals
|
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 |
|
r-minionqc
|
public |
Quality control for MinION sequencing 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 |
|
srnamapper
|
public |
Mapping small RNA data to a genome.
|
2024-12-13 |
|
distle
|
public |
Fast distance matrix calculations on fasta and cgmlst files
|
2024-12-13 |
|
ucsc-fanoise
|
public |
Add noise to .fa file
|
2024-12-13 |
|
hi-corrector
|
public |
Remove biases from chromatin contact matrices generated by genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC
|
2024-12-13 |
|
jarvis
|
public |
Efficient lossless compression of genomic sequences
|
2024-12-13 |
|
chromap
|
public |
Fast alignment and preprocessing of chromatin profiles
|
2024-12-13 |
|
ucsc-htmlcheck
|
public |
Do a little reading and verification of html file
|
2024-12-13 |
|
simba_pbg
|
public |
A customized PyTorch-BigGraph (PBG) package for `simba`
|
2024-12-13 |
