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ucsc-splitfilebycolumn
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public |
Split text input into files named by column value
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2024-12-14 |
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phylocsfpp
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public |
A fast and user-friendly implementation of PhyloCSF with annotation tools.
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2024-12-14 |
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pretextmap
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public |
Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
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2024-12-14 |
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r-saige
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public |
SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016)
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2024-12-14 |
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stringdecomposer
|
public |
A tool for decomposing of strings into a set of given monomers
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2024-12-14 |
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ucsc-axttomaf
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public |
Convert from axt to maf format
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2024-12-14 |
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ucsc-coltransform
|
public |
Add and/or multiply column by constant.
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2024-12-14 |
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boms
|
public |
Cell Segmentation for Spatial Transcriptomics Data using BOMS
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2024-12-14 |
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illumina-interop
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public |
The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. These metric files are binary files produced during a run providing detailed statistics about a run. In a few cases, the metric files are produced after a run during secondary analysis (index metrics) or for faster display of a subset of the original data (collapsed quality scores).
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2024-12-14 |
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shark
|
public |
Mapping-free filtering of useless RNA-Seq reads
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2024-12-14 |
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akt
|
public |
Ancestry and Kinship Tools (AKT)
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2024-12-14 |
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reads2graph
|
public |
reads2graph is an efficient tool for constructing edit-distance-based read graph from short-read sequencing data.
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2024-12-14 |
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dashing
|
public |
Fast and accurate genomic distances using HyperLogLog
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2024-12-14 |
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reseq
|
public |
ReSeq Illumina/BGI simulator
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2024-12-14 |
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ucsc-mafaddirows
|
public |
add 'i' rows to a maf
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2024-12-14 |
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zorro
|
public |
ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple sequence alignment.
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2024-12-14 |
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libgtextutils
|
public |
No Summary
|
2024-12-14 |
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coatran
|
public |
Coalescent tree simulation along a transmission network
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2024-12-14 |
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ucsc-maforder
|
public |
order components within a maf file
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2024-12-14 |
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maast
|
public |
Microbial agile accurate SNP Typer
|
2024-12-14 |
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sciphi
|
public |
Single-cell mutation identification via phylogenetic inference
|
2024-12-14 |
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r-cleangeostreamr
|
public |
Automatic curation of spatially annotated data.
|
2024-12-14 |
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ucsc-parahub
|
public |
parasol hub server version 12.18
|
2024-12-14 |
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perl-padwalker
|
public |
play with other peoples' lexical variables
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2024-12-14 |
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bambamc
|
public |
lightweight C implementation of name collating BAM file input and BAM file output
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2024-12-14 |
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libstatgen
|
public |
Useful set of classes for creating statistical genetic programs.
|
2024-12-14 |
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svict
|
public |
SViCT is a computational tool for detecting structural variations from cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA).
|
2024-12-14 |
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pb-dazzler
|
public |
The Dresden Assembler suite -- Pacific Biosciences forks
|
2024-12-14 |
|
perl-set-object
|
public |
Unordered collections (sets) of Perl Objects
|
2024-12-14 |
|
swipe
|
public |
Tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.
|
2024-12-14 |
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ucsc-nibfrag
|
public |
Extract part of a nib file as .fa (all bases/gaps lower case by default)
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2024-12-14 |
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ucsc-checktablecoords
|
public |
check invariants on genomic coords in table(s).
|
2024-12-14 |
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ucsc-pslpostarget
|
public |
flip psl strands so target is positive and implicit
|
2024-12-14 |
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r-phyext2
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public |
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
|
2024-12-14 |
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bcalm
|
public |
BCALM 2 is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.
|
2024-12-14 |
|
paladin
|
public |
Protein Alignment and Detection Interface
|
2024-12-14 |
|
scrappie
|
public |
Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
|
2024-12-14 |
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ucsc-pslpairs
|
public |
join paired ends in psl alignments
|
2024-12-14 |
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metacortex
|
public |
MetaCortex is an assembler for metagenomic, or environmental sequence data.
|
2024-12-14 |
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pbpigeon
|
public |
PacBio transcript toolkit
|
2024-12-14 |
|
splitmem
|
public |
Graphical pan-genome analysis with suffix skips
|
2024-12-14 |
|
qgrs-cpp
|
public |
C++ implementation of QGRS mapping.
|
2024-12-14 |
|
readfq
|
public |
A high-speed tool to calculate reads number and total base count in FASTQ file, forked from Li Heng's original version
|
2024-12-14 |
|
r-ggbiplot
|
public |
A biplot based on ggplot2
|
2024-12-14 |
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primer3-py
|
public |
Python bindings for Primer3
|
2024-12-14 |
|
r-anndata
|
public |
A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
|
2024-12-14 |
|
ucsc-maffetch
|
public |
get overlapping records from an MAF using an index table
|
2024-12-14 |
|
fairy
|
public |
fairy calculates all-to-all approximate coverage for multi-sample metagenomic binning > 100x faster than alignment.
|
2024-12-14 |
|
lrez
|
public |
Standalone tool and library allowing to work with barcoded linked-reads
|
2024-12-14 |
|
r-phewas
|
public |
Phenome Wide Association Studies (PheWAS) - Functions to perform Phenome Wide Association Studies (PheWAS). These functions include the conversion of ICD9 codes to PheWAS codes (v1.2), statistical analysis, and plotting.
|
2024-12-14 |
