116 tool(s) found

Tool Description Topics Available version(s)
AnnotateBed annotate coverage of features from multiple files 16
Annotates the depth & breadth of coverage of features from multiple files 1
BAM to BED converter 20
BED to BAM converter 17
BED to IGV create batch script for taking IGV screenshots 9
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 16
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 3
BEDPE to BAM converter 17
BedToIntervalList convert coordinate data into picard interval list format 9
bigWigToBedGraph Convert from bigWig to bedGraph format 3
bowtie-to-bed converter 1
ClosestBed find the closest, potentially non-overlapping interval 16
ClusterBed cluster overlapping/nearby intervals 16
ComplementBed Extract intervals not represented by an interval file 17
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
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 16
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 16
FlankBed create new intervals from the flanks of existing intervals 17
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 17
GetFastaBed use intervals to extract sequences from a FASTA file 16
GFF-to-BED converter Conversion 1
GFF-to-BED converter 2
GroupByBed group by common cols and summarize other cols 16
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 16
Intersect multiple sorted BED files 20
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 16
LAV to BED Converts a LAV formatted file to BED format 1
LinksBed create a HTML page of links to UCSC locations 16
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 7
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 7
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 8
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 7
MAF to BED Converts a MAF formatted file to the BED format 1
MakeWindowsBed make interval windows across a genome 17
Map peptides to a bed file for viewing in a genome browser 2
MapBed apply a function to a column for each overlapping interval 16
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 16
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge BedGraph files 4
MergeBED combine overlapping/nearby intervals into a single interval 16
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
NucBed profile the nucleotide content of intervals in a FASTA file 16
Nucleotide subsequence search providing regions in BED format 2
OverlapBed computes the amount of overlap from two intervals 16
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 17
ReldistBed calculate the distribution of relative distances 16
ShuffleBed randomly redistrubute intervals in a genome 17
SlopBed adjust the size of intervals 17
SortBED order the intervals 16
SpacingBed reports the distances between features 12
Stitch Gene blocks given a set of coding exon intervals 1
SubtractBed remove intervals based on overlaps 16
TagBed tag BAM alignments based on overlaps with interval files 16
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 16