120 tool(s) found

Tool Description Topics Available version(s)
Annotates the depth & breadth of coverage of features from multiple files 1
bed to protein map genomic location of proteins for MVP 2
BED-to-bigBed converter Conversion 2
BED-to-GFF converter 2
BED-to-GFF converter Conversion 1
bed_clean clean up BED files 1
bed_closest find closest intervals 1
bed_collapse collapse intervals 1
bed_intersect intersect two interval sets 1
bed_overlap_significance significance of two interval sets overlapping 1
bed_resize change interval size 1
bed_shuffle shuffle intervals chromosome not weighted by length 1
bed_size_stat plot interval size distribution 1
bed_sort_with_header sort intervals with header lines 1
bed_to_bigwig make bigwig from BED or BAM 1
bed_window make a window around interval center 1
BedCov calculate read depth for a set of genomic intervals 5
bedgraph-to-bigwig converter 1
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
bigWigToBedGraph Convert from bigWig to bedGraph format 2
bowtie-to-bed converter 1
Cluster, infer trajectories and embed with scanpy 7
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Concatenate two BED files Aggregation 6
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert from BAM to FastQ 13
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert gffCompare annotated GTF to BED for StringTie results 4
Convert GTF to BED12 1
Convert lped to plink pbed 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Count intervals in one file overlapping intervals in another file 2
Create a BedGraph of genome coverage 3
Create a histogram of genome coverage 3
CrossMap BED Convert genome coordinates or annotation files between genome assemblies 5
Cytosine Report To Bedgraphs Converts genome-wide cytosine methylation report to Bedgraphs 1
dNdS Report Calculate the dN/dS value for each region in a bed file 2
Extract nucleotide range and flanking sequences Get FASTA sequences from BED interval 1
extract-boxed-sequences Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility 2
extract_fastasequence using BED file 1
Fasta to Bed File Create Bed file from Multiple fasta file 1
fastSTRUCTURE. Step 1: BED, BIM and FAM file calculation 1
Filter BED on splice junctions that are not in a reference bed file 1
filter-annotated-entries Split entries into two files based on whether they overlap annotations in a bed file 2
Find Nested Alternate ORFs (nAlt-ORFs) from BED and 2bit/FASTA Coding region prediction Codon usage analysis Codon usage table generation Genome annotation 1
Gene BED To Exon/Intron/Codon BED expander 1
Generate BED file for a list of genes 1
GetFastaBed use intervals to extract sequences from a FASTA file 20
GFF-to-BED converter 2
GFF-to-BED converter Conversion 1
GraphEmbed Compute and plot a 2D embedding of a data matrix given supervised class information 1
GTF-to-BEDGraph converter Conversion 1
homer_bed2pos 1
homer_pos2bed 1
idpEmbedder Embed human/mouse gene metadata into IDPicker files 4
Intersect BAM alignments with intervals in another files 2
Intersect intervals find overlapping intervals in various ways 22
LAV to BED Converts a LAV formatted file to BED format 1
MACS2 bdgbroadcall Call broad peaks from bedGraph output 9
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 9
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 10
MACS2 bdgpeakcall Call peaks from bedGraph output 9
MAF to BED Converts a MAF formatted file to the BED format 1
Map peptides to a bed file for viewing in a genome browser 3
MapBed apply a function to a column for each overlapping interval 21
mapper analyzer Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. 1
Merge BedGraph files 3
NucBed profile the nucleotide content of intervals in a FASTA file 21
Nucleotide subsequence search providing regions in BED format 2
proBAMconvert peptide identifications to proBAM or proBED 1
QCEmbedder Attaches a table or an image to a given qc parameter. 4
qiime2 diversity tsne t-distributed stochastic neighbor embedding 2
Scanpy PlotEmbed visualise cell embeddings 12
snp location to bed format convert SNP to interval 1
Stitch Gene blocks given a set of coding exon intervals 4
Translate BED Sequences 3 frame translation of BED augmented with a sequence column 1
Translate BED transcripts cDNA in 3frames or CDS 1
VCF-BEDintersect: Intersect VCF and BED datasets 5
vcf-to-bigwig converter 1
VCFannotate: Intersect VCF records with BED annotations 5
Wig/BedGraph-to-bigWig converter 2