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telseq
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public |
A software for calculating telomere length
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2024-12-14 |
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perl-namespace-autoclean
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public |
Keep imports out of your namespace
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2024-12-14 |
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perl-string-approx
|
public |
No Summary
|
2024-12-14 |
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fann
|
public |
No Summary
|
2024-12-14 |
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bioawk
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public |
BWK awk modified for biological data
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2024-12-14 |
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ucsc-genepredhisto
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public |
get data for generating histograms from a genePred file.
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2024-12-14 |
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rna-seqc
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public |
Fast, efficient RNA-Seq metrics for quality control and process optimization.
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2024-12-14 |
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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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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.
|
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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akt
|
public |
Ancestry and Kinship Tools (AKT)
|
2024-12-14 |
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ucsc-mafaddirows
|
public |
add 'i' rows to a maf
|
2024-12-14 |
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libgtextutils
|
public |
No Summary
|
2024-12-14 |
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ucsc-maforder
|
public |
order components within a maf file
|
2024-12-14 |
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ucsc-parahub
|
public |
parasol hub server version 12.18
|
2024-12-14 |
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pasta
|
public |
An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm
|
2024-12-14 |
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perl-padwalker
|
public |
play with other peoples' lexical variables
|
2024-12-14 |
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bambamc
|
public |
lightweight C implementation of name collating BAM file input and BAM file output
|
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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pb-dazzler
|
public |
The Dresden Assembler suite -- Pacific Biosciences forks
|
2024-12-14 |
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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
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public |
Extract part of a nib file as .fa (all bases/gaps lower case by default)
|
2024-12-14 |
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rnastructure
|
public |
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
|
2024-12-14 |
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ucsc-checktablecoords
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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
|
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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splitmem
|
public |
Graphical pan-genome analysis with suffix skips
|
2024-12-14 |
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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 |
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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 |
|
ucsc-maffetch
|
public |
get overlapping records from an MAF using an index table
|
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 |
|
soapdenovo2-errorcorrection
|
public |
Error correction for soapdenovo2.
|
2024-12-14 |
|
gb_taxonomy_tools
|
public |
These are four simple utilities which perform certain manipulations and visualization tasks on GenBank taxonomic information.
|
2024-12-14 |
|
seqan_tcoffee
|
public |
SeqAn::T-Coffee - Multiple Sequence Alignment
|
2024-12-14 |
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kronik
|
public |
No Summary
|
2024-12-14 |
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rapmap
|
public |
Rapid sensitive and accurate read mapping via quasi-mapping
|
2024-12-14 |
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ucsc-bedcoverage
|
public |
Analyse coverage by bed files - chromosome by
|
2024-12-14 |
|
fsm-lite
|
public |
Frequency-based String Mining (lite)
|
2024-12-14 |
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matlock
|
public |
Simple tools for working with Hi-C data
|
2024-12-14 |
|
ucsc-chainstitchid
|
public |
Join chain fragments with the same chain ID into a single
|
2024-12-14 |
|
transgenescan
|
public |
Software tool for finding genes in assembled transcripts from metatranscriptomic sequences.
|
2024-12-14 |
|
gatb
|
public |
The Genome Analysis Toolbox with de-Bruijn graph
|
2024-12-14 |
|
libidn
|
public |
No Summary
|
2024-12-14 |
|
r-spieceasi
|
public |
Estimate networks from the precision matrix of compositional microbial abundance data.
|
2024-12-14 |
