116 tool(s) found

Tool Description Topics Available version(s)
AnnotateBed annotate coverage of features from multiple files 17
Annotates the depth & breadth of coverage of features from multiple files 1
BAM to BED converter 21
BED to BAM converter 18
BED to IGV create batch script for taking IGV screenshots 10
bed to protein map genomic location of proteins for MVP 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
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_to_GFF3 converter 3
bed_window make a window around interval center 1
BedCov calculate read depth for a set of genomic intervals 4
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
bigWigToBedGraph Convert from bigWig to bedGraph format 3
bowtie-to-bed converter 1
ClosestBed find the closest, potentially non-overlapping interval 17
ClusterBed cluster overlapping/nearby intervals 17
ComplementBed Extract intervals not represented by an interval file 18
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert bed/bim/fam to ped/map 1
Convert bim/fam/bed to VCF 1
Convert FindPeaks output (.peaks) into Bed 1
Convert from BAM to FastQ 14
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert gffCompare annotated GTF to BED for StringTie results 1
Convert GTF to BED12 1
Convert lped to plink pbed 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Count intervals in one file overlapping intervals in another file 3
Create a BedGraph of genome coverage 4
Create a histogram of genome coverage 4
CrossMap BED Convert genome coordinates or annotation files between genome assemblies 1
edgeR: Convert 'differentially expressed genes'-table to bedgraph(s) EdgeR's "differentially expressed genes" table to bedgraph(s) 2
ExpandBed replicate lines based on lists of values in columns 17
Extract central region for a bed file 1
extract-boxed-sequences Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility 3
Fasta from bed Get Fasta sequences from a bed and a fasta file 1
fastaFromBed 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 3
FisherBed calculate Fisher statistic between two feature files 17
FlankBed create new intervals from the flanks of existing intervals 18
Gene BED To Exon/Intron/Codon BED expander 1
Generate BED file for a list of genes 1
Genome Coverage compute the coverage over an entire genome 18
GetFastaBed use intervals to extract sequences from a FASTA file 17
GFF-to-BED converter Conversion 1
GFF-to-BED converter 2
GroupByBed group by common cols and summarize other cols 17
GTF-to-BEDGraph converter Conversion 1
homer_bed2pos 1
homer_pos2bed 1
idpEmbedder Embed human/mouse gene metadata into IDPicker files 2
IGV2Gistic Converts an IGV formatted segment file into an GISTIC2.0 compatible segment file. Requires exon BED file. Also produces an accompanying marker file in order to run GISTIC2.0. 1
Intersect BAM alignments with intervals in another files 3
Intersect intervals find overlapping intervals in various ways 17
intersectBed report overlaps between two feature files 1
intersectBed Report overlaps between two feature files. 1
JaccardBed calculate the distribution of relative distances between two files 17
LAV to BED Converts a LAV formatted file to BED format 1
LinksBed create a HTML page of links to UCSC locations 17
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MAF to BED Converts a MAF formatted file to the BED format 1
MakeWindowsBed make interval windows across a genome 18
Map peptides to a bed file for viewing in a genome browser 2
MapBed apply a function to a column for each overlapping interval 17
mapper analyzer Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. 1
MaskFastaBed use intervals to mask sequences from a FASTA file 17
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge BedGraph files 4
MergeBED combine overlapping/nearby intervals into a single interval 17
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multiple Intersect identifies common intervals among multiple interval files 21
NucBed profile the nucleotide content of intervals in a FASTA file 17
Nucleotide subsequence search providing regions in BED format 2
OverlapBed computes the amount of overlap from two intervals 17
plink: ped2bed Convert ped to bed 2
QCEmbedder Attaches a table or an image to a given qc parameter. 2
RandomBed generate random intervals in a genome 18
ReldistBed calculate the distribution of relative distances 17
ShuffleBed randomly redistrubute intervals in a genome 18
SlopBed adjust the size of intervals 18
SortBED order the intervals 17
SpacingBed reports the distances between features 13
Stitch Gene blocks given a set of coding exon intervals 1
SubtractBed remove intervals based on overlaps 17
TagBed tag BAM alignments based on overlaps with interval files 17
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 6
VCFannotate: Intersect VCF records with BED annotations 6
Wig/BedGraph-to-bigWig converter 2
WigMaker for BED files 1
WindowBed find overlapping intervals within a window around an interval 17