|
dsk
|
public |
DSK is a k-mer counter for reads or genomes.
|
2024-12-13 |
|
ptrimmer
|
public |
Used to trim off the primer sequence from mutiplex amplicon sequencing
|
2024-12-13 |
|
ucsc-psltochain
|
public |
Convert psl records to chain records
|
2024-12-13 |
|
cd-hit
|
public |
Clusters and compares protein or nucleotide sequences
|
2024-12-13 |
|
guide-counter
|
public |
Fast and accurate guide counting for CRISPR screens
|
2024-12-13 |
|
humid
|
public |
HUMID -- High-performance UMI Deduplicator
|
2024-12-13 |
|
mvicuna
|
public |
M-Vicuna is a modularized version of VICUNA, a de novo assembly program targeting populations with high mutation rates
|
2024-12-13 |
|
xs-sim
|
public |
Simulates NGS reads
|
2024-12-13 |
|
sparc
|
public |
No Summary
|
2024-12-13 |
|
verse
|
public |
VERSE: a versatile and efficient RNA-Seq read counting tool
|
2024-12-13 |
|
lordfast
|
public |
Sensitive and Fast Alignment Search Tool for Long Read sequencing Data
|
2024-12-13 |
|
mmquant
|
public |
RNA-Seq quantification tool, with special handling on multi-mapping reads.
|
2024-12-13 |
|
scelestial
|
public |
Scelestial, Single Cell Lineage Tree Inference based on a Steiner Tree Approximation Algorithm
|
2024-12-13 |
|
r-loomr
|
public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based
format for storing and interacting with large single-cell RNAseq datasets. loomR
provides an interface for working with loom files in a loom-specific way; we provide
routines for validating loom files, iterating with chunks through data within the
loom file, and provide a platform for other packages to build support for loom files.
|
2024-12-13 |
|
shapeit4
|
public |
fast and accurate method for estimation of haplotypes (phasing)
|
2024-12-13 |
|
altair-mf
|
public |
Software for alignment-free and spatial-temporal analysis of multi-FASTA data
|
2024-12-13 |
|
ucsc-tolower
|
public |
Convert upper case to lower case in file. Leave other chars alone
|
2024-12-13 |
|
anise_basil
|
public |
BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. ANISE is a method for the assembly of large insertions from paired reads in BAM format and a list candidate insert breakpoints as generated by BASIL.
|
2024-12-13 |
|
mapdia
|
public |
Performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.
|
2024-12-13 |
|
red
|
public |
Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
|
2024-12-13 |
|
rasusa
|
public |
Randomly subsample sequencing reads or alignments
|
2024-12-13 |
|
hapbin
|
public |
hapbin is a collection of tools for efficiently calculating Extended Haplotype Homozygosity (EHH), the Integrated Haplotype Score (iHS) and the Cross Population Extended Haplotype Homozogysity (XP-EHH) statistic.
|
2024-12-13 |
|
r-misha
|
public |
Toolkit for analysis of genomic data
|
2024-12-13 |
|
ucsc-addcols
|
public |
Sum columns in a text file.
|
2024-12-13 |
|
graphtyper
|
public |
Population-scale genotyping using pangenome graphs
|
2024-12-13 |
|
ucsc-avecols
|
public |
average together columns
|
2024-12-13 |
|
sequali
|
public |
Fast sequencing quality metrics
|
2024-12-13 |
|
ucsc-chainsplit
|
public |
Split chains up by target or query sequence
|
2024-12-13 |
|
r-cssam
|
public |
Cell-type specific differential expression of a microarray experiment of heterogeneous tissue samples, using SAM.
|
2024-12-13 |
|
ucsc-fapolyasizes
|
public |
get poly A sizes
|
2024-12-13 |
|
rust-ncbitaxonomy
|
public |
A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering.
|
2024-12-13 |
|
ucsc-hgbbidblink
|
public |
Add table that just contains a pointer to a bbiFile to database. This program
|
2024-12-13 |
|
ucsc-mktime
|
public |
convert date string to unix timestamp
|
2024-12-13 |
|
trimal
|
public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
|
2024-12-13 |
|
miniprot
|
public |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
|
2024-12-13 |
|
racon
|
public |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
|
2024-12-13 |
|
r-xmlrpc
|
public |
A simple implementation of XML-RPC for R.
|
2024-12-13 |
|
ucsc-pslswap
|
public |
Swap target and query in psls
|
2024-12-13 |
|
proda
|
public |
ProDA - Multiple alignment of protein sequences with repeated and shuffled elements
|
2024-12-13 |
|
ucsc-ratotab
|
public |
Convert ra file to table.
|
2024-12-13 |
|
ucsc-fetchchromsizes
|
public |
used to fetch chrom.sizes information from UCSC for the given <db>
|
2024-12-13 |
|
ucsc-nibsize
|
public |
print size of nibs
|
2024-12-13 |
|
mtsv-tools
|
public |
mtsv_tools contains core tools for alignment-based metagenomic binning
|
2024-12-13 |
|
hmmer
|
public |
Biosequence analysis using profile hidden Markov models
|
2024-12-13 |
|
peer
|
public |
A collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods
|
2024-12-13 |
|
oarfish
|
public |
oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data
|
2024-12-13 |
|
mummer
|
public |
MUMmer is a system for rapidly aligning entire genomes
|
2024-12-13 |
|
amplici
|
public |
AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs.
|
2024-12-13 |
|
ucsc-hgfakeagp
|
public |
Create fake AGP file by looking at N's
|
2024-12-13 |
|
alcor
|
public |
Software for alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.
|
2024-12-13 |
