adapterremoval
|
public |
The AdapterRemoval v2 tool for merging and clipping reads.
|
2024-12-12 |
ucsc-bigwigcat
|
public |
merge non-overlapping bigWig files
|
2024-12-12 |
ucsc-pslselect
|
public |
select records from a PSL file.
|
2024-12-12 |
ucsc-bigwigmerge
|
public |
Merge together multiple bigWigs into a single output bedGraph.
|
2024-12-12 |
ucsc-pslmrnacover
|
public |
Make histogram of coverage percentage of mRNA in psl.
|
2024-12-12 |
ucsc-mafspeciessubset
|
public |
Extract a maf that just has a subset of species.
|
2024-12-12 |
fastq-and-furious
|
public |
Fast handling of FASTQ files
|
2024-12-12 |
ucsc-hgloadnet
|
public |
Load a generic net file into database
|
2024-12-12 |
tantan
|
public |
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
|
2024-12-12 |
ucsc-hgloadout
|
public |
load RepeatMasker .out files into database
|
2024-12-12 |
r-biodb
|
public |
An R package for connecting to chemical and biological databases.
|
2024-12-12 |
gffcompare
|
public |
GffCompare by Geo Pertea
|
2024-12-12 |
boutroslabplottinggeneral
|
public |
No Summary
|
2024-12-12 |
ucsc-fastqtofa
|
public |
Convert from fastq to fasta format.
|
2024-12-12 |
ucsc-hgloadmaf
|
public |
Load a maf file index into the database
|
2024-12-12 |
ucsc-mafaddqrows
|
public |
Add quality data to a maf
|
2024-12-12 |
ucsc-mafsinregion
|
public |
Extract MAFS in a genomic region
|
2024-12-12 |
ucsc-farc
|
public |
Reverse complement a FA file
|
2024-12-12 |
ucsc-maftosnpbed
|
public |
finds SNPs in MAF and builds a bed with their functional consequence
|
2024-12-12 |
ucsc-maskoutfa
|
public |
Produce a masked .fa file given an unmasked .fa and
|
2024-12-12 |
ucsc-gff3topsl
|
public |
convert a GFF3 CIGAR file to a PSL file
|
2024-12-12 |
links
|
public |
Long Interval Nucleotide K-mer Scaffolder
|
2024-12-12 |
daligner
|
public |
DALIGNER: Find all significant local alignments between reads
|
2024-12-12 |
blockbuster
|
public |
Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.
|
2024-12-12 |
ucsc-transmappsltogenepred
|
public |
convert PSL alignments of mRNAs to gene annotations.
|
2024-12-12 |
wtdbg
|
public |
Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
|
2024-12-12 |
survivor
|
public |
Toolset for SV simulation, comparison and filtering
|
2024-12-12 |
netcdf-metadata-info
|
public |
Metadata information from netcdf file for Galaxy use.
|
2024-12-12 |
bwa
|
public |
The BWA read mapper.
|
2024-12-12 |
fermi
|
public |
A WGS de novo assembler based on the FMD-index for large genomes
|
2024-12-12 |
cmph
|
public |
No Summary
|
2024-12-12 |
merfishtools
|
public |
MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.
|
2024-12-12 |
bgt
|
public |
Flexible genotype query among 30,000+ samples whole-genome.
|
2024-12-12 |
ucsc-bigmaftomaf
|
public |
convert bigMaf to maf file
|
2024-12-12 |
ucsc-bigbednameditems
|
public |
Extract item of given name from bigBed
|
2024-12-12 |
conus
|
public |
CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.
|
2024-12-12 |
dazz_db
|
public |
DAZZ_DB: The Dazzler Data Base
|
2024-12-12 |
ucsc-bigwiginfo
|
public |
Print out information about bigWig file.
|
2024-12-12 |
simwalk2
|
public |
Stochastic Statistical Analysis of Qualitative Traits
|
2024-12-12 |
fastq-multx
|
public |
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.
|
2024-12-12 |
ucsc-bedsort
|
public |
Sort a .bed file by chrom,chromStart
|
2024-12-12 |
ucsc-rowstocols
|
public |
Convert rows to columns and vice versa in a text file.
|
2024-12-12 |
r-sbpiper
|
public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
|
2024-12-12 |
ucsc-overlapselect
|
public |
Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range.
|
2024-12-12 |
ucsc-spacedtotab
|
public |
Convert fixed width space separated fields to tab separated
|
2024-12-12 |
ema
|
public |
Fast & accurate alignment of barcoded short-reads
|
2024-12-12 |
dwgsim
|
public |
Whole Genome Simulator for Next-Generation Sequencing
|
2024-12-12 |
r-mcpcounter
|
public |
Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression
|
2024-12-12 |
ucsc-xmltosql
|
public |
Convert XML dump into a fairly normalized relational database
|
2024-12-12 |
ucsc-pslfilter
|
public |
filter out psl file
|
2024-12-12 |