Repositories Owned by devteam
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Synopsis
Type
Metadata
Revisions
Category
add_value
Add a value as a new column.
Unrestricted
4 (2023-09-29)
3 (2015-11-11)
Text Manipulation
all_cufflinks_tool_suite
Contains the full set of cuff* tools.
Repository suite definition
4
(2015-11-02)
Transcriptomics
all_vcftools
A metapackage that will install all vcftools wrappers and dependencies.
Repository suite definition
0
(2013-11-26)
Variant Analysis
analyze_covariates
Analyze Covariates - draw plots
Unrestricted
2
(2014-04-02)
Sequence Analysis
annotation_profiler
Profile Annotations for a set of genomic intervals
Unrestricted
0
(2014-05-19)
not set
a_selenium_test_repo
Repository for testing installation, uninstallation, and upgrades
Unrestricted
1 (2020-04-20)
0 (2020-04-17)
not set
bamleftalign
A utility for leftaligning indels in BAM datasets
Unrestricted
0
(2014-06-24)
Sequence Analysis
Variant Analysis
bamtools
Operate on and transform BAM datasets in various ways using bamtools
Unrestricted
8 (2024-03-15)
7 (2023-01-13)
6 (2023-01-11)
5 (2021-11-27)
4 (2019-12-04)
3 (2017-01-18)
2 (2015-11-11)
1 (2015-08-26)
Sequence Analysis
bamtools_filter
Filter BAM datasets on various attributes using bamtools filter
Unrestricted
11 (2024-03-15)
10 (2023-01-13)
9 (2021-11-27)
8 (2020-02-20)
4 (2017-01-18)
3 (2017-01-13)
1 (2015-03-09)
Sequence Analysis
bamtools_split
Wrapper for bamtools split application Split.
Unrestricted
5 (2023-01-11)
4 (2021-11-27)
3 (2019-12-04)
2 (2017-01-18)
1 (2015-11-11)
0 (2015-01-09)
Sequence Analysis
bam_to_sam
Converts BAM format to SAM format.
Unrestricted
9 (2024-09-08)
7 (2021-09-28)
6 (2018-10-14)
4 (2015-04-21)
3 (2015-03-18)
2 (2015-03-05)
0 (2013-08-26)
SAM
basecoverage
Base Coverage of all intervals
Unrestricted
6 (2022-06-13)
3 (2015-11-11)
0 (2014-04-01)
Genomic Interval Operations
best_regression_subsets
Perform Best-subsets Regression
Unrestricted
2 (2014-04-10)
1 (2014-04-03)
Sequence Analysis
Variant Analysis
blast_datatypes
BlastXml and other blast datatypes
Unrestricted
11 (2015-09-04)
2 (2012-09-20)
1 (2012-08-23)
Sequence Analysis
blat_coverage_report
Polymorphism of the Reads
Unrestricted
0
(2014-05-19)
not set
blat_mapping
Coverage of the Reads in wiggle format
Unrestricted
0
(2014-05-19)
not set
bowtie2
Bowtie2: Fast and sensitive read alignment
Unrestricted
32 (2024-05-13)
31 (2024-02-26)
30 (2022-11-03)
29 (2022-07-06)
28 (2022-01-31)
27 (2021-07-10)
25 (2019-08-23)
24 (2019-04-04)
23 (2018-06-06)
21 (2018-04-10)
19 (2018-01-20)
18 (2017-11-24)
17 (2017-11-14)
15 (2017-06-01)
14 (2017-04-12)
13 (2017-01-09)
12 (2017-01-08)
11 (2017-01-03)
10 (2016-03-22)
9 (2015-11-18)
8 (2015-11-16)
7 (2015-11-11)
4 (2015-07-21)
3 (2015-03-09)
2 (2014-12-12)
1 (2014-03-05)
Next Gen Mappers
bowtie_color_wrappers
Galaxy wrappers for the Bowtie short read mapping tools on color space reads
Unrestricted
4
(2015-07-21)
Next Gen Mappers
bowtie_wrappers
Galaxy wrappers for the Bowtie short read mapping tools.
Unrestricted
8 (2017-05-15)
7 (2017-05-04)
5 (2016-08-18)
4 (2015-07-21)
3 (2014-02-21)
Next Gen Mappers
bwa
Wrapper for bwa mem, aln, sampe, and samse
Unrestricted
28 (2025-03-24)
27 (2025-03-19)
25 (2022-08-19)
24 (2021-05-05)
23 (2020-05-19)
19 (2017-12-22)
17 (2017-11-21)
15 (2017-09-30)
14 (2017-06-01)
13 (2017-01-30)
11 (2016-01-19)
10 (2016-01-08)
9 (2015-12-03)
8 (2015-11-11)
6 (2015-07-21)
5 (2015-07-21)
4 (2015-06-18)
3 (2015-03-20)
2 (2015-03-20)
1 (2015-01-14)
Next Gen Mappers
bwa_wrappers
Galaxy wrappers for the BWA short read aligner.
Unrestricted
3
(2014-01-16)
Next Gen Mappers
canonical_correlation_analysis
Canonical Correlation Analysis
Unrestricted
0
(2014-05-19)
not set
categorize_elements_satisfying_criteria
Categorize Elements satisfying criteria.
Unrestricted
0
(2013-09-25)
Statistics
ccat
Control-based ChIP-seq Analysis Tool
Unrestricted
2 (2021-12-03)
1 (2015-07-21)
ChIP-seq
cd_hit_dup
simple tool for removing duplicates from sequencing reads
Unrestricted
1
(2015-07-21)
Metagenomics
Sequence Analysis
change_case
Convert column case.
Unrestricted
3
(2015-11-11)
Text Manipulation
clustalw
ClustalW multiple sequence alignment program for DNA or proteins
Unrestricted
7 (2023-11-02)
3 (2017-05-22)
2 (2015-10-09)
Sequence Analysis
Fasta Manipulation
cluster
Cluster the intervals of a dataset
Unrestricted
5 (2022-06-13)
3 (2015-11-11)
0 (2014-04-01)
Genomic Interval Operations
column_maker
Compute an expression on every row
Unrestricted
10 (2024-08-22)
9 (2022-07-28)
8 (2021-03-09)
6 (2021-01-25)
5 (2020-12-30)
4 (2020-07-15)
3 (2020-06-04)
2 (2018-10-25)
1 (2015-11-11)
Text Manipulation
complement
Complement intervals of a dataset
Unrestricted
5 (2022-06-13)
3 (2015-11-11)
0 (2014-04-01)
Genomic Interval Operations
compute_motif_frequencies_for_all_motifs
Compute Motif Frequencies For All Motifs, motif by motif.
Unrestricted
1
(2015-11-11)
Sequence Analysis
Statistics
compute_motifs_frequency
Compute Motif Frequencies in indel flanking regions.
Unrestricted
1
(2015-11-11)
Sequence Analysis
Statistics
compute_q_values
Compute q-values based on multiple simultaneous tests p-values
Unrestricted
2
(2015-11-11)
Sequence Analysis
Variant Analysis
concat
Concatenate two bed files
Unrestricted
5 (2022-06-13)
2 (2015-11-11)
Genomic Interval Operations
condense_characters
Condense consecutive characters.
Unrestricted
2
(2015-07-21)
Text Manipulation
convert_characters
Convert delimiters to tab.
Unrestricted
3 (2020-07-06)
2 (2015-07-21)
Text Manipulation
convert_solid_color2nuc
Convert Color Space to Nucleotides
Unrestricted
0
(2014-05-19)
not set
correlation
Correlation for numeric columns
Unrestricted
0
(2014-07-28)
Statistics
count_covariates
Count Covariates on BAM files
Unrestricted
0
(2014-04-01)
Sequence Analysis
count_gff_features
Count GFF Features
Unrestricted
1 (2017-06-06)
0 (2014-07-28)
Sequence Analysis
coverage
Coverage of a set of intervals on second set of intervals
Unrestricted
4 (2022-06-13)
2 (2015-11-11)
0 (2014-04-01)
Genomic Interval Operations
ctd_batch
CTD analysis of chemicals, diseases, or genes
Unrestricted
0
(2013-09-25)
Sequence Analysis
cuffcompare
Galaxy wrappers for the Cuffcompare tool.
Unrestricted
11 (2024-10-05)
10 (2020-06-16)
9 (2017-02-19)
8 (2017-02-07)
5 (2014-01-09)
3 (2013-12-04)
2 (2013-12-04)
1 (2013-10-01)
Transcriptomics
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