@@ -3,88 +3,22 @@ id: tool-index
33title : Tool Index (A-Z)
44sidebar_label : Tool Index (A-Z)
55---
6+ import { PesterDataTable } from "@site/src /components/PesterDataTable";
7+ import { columns, toolIndex, moduleTests } from "./toolIndex.table";
68
7- _ The full list of ScriptManager tools_
9+ ### Tool Index
10+ The full list of ScriptManager tools. It's sortable! Click the headers!
811
9- <!-- -`gene-track` (suspended)\--->
10- <!-- -\`peak-pair` (suspended)\--->
11- <!-- -\[similarity-matrix](https://github.com/CEGRcode/scriptmanager/wiki/Read-Analysis#similarity-matrix-suspended) (suspended)\--->
12+ <PesterDataTable
13+ columns={columns}
14+ data={ toolIndex }
15+ />
1216
13- | Tool Name | Tool Group | Description |
14- | ------------- | : ------------- :| ------------- |
15- | [ ` aggregate-data ` ] [ aggregate-data ] | Read Analysis | _ description_ |
16- | [ ` bam-correlation ` ] [ bam-correlation ] | BAM Statistics | _ description_ |
17- | [ ` bam-indexer ` ] [ bam-indexer ] | BAM Manipulation | GUI only! _ description_ |
18- | [ ` bam-to-bedgraph ` ] [ bam-to-bedgraph ] | BAM Format Converter | _ description_ |
19- | [ ` bam-to-bed ` ] [ bam-to-bed ] | BAM Format Converter | _ description_ |
20- | [ ` bam-to-gff ` ] [ bam-to-gff ] | BAM Format Converter | _ description_ |
21- | [ ` bam-to-scidx ` ] [ bam-to-scidx ] | BAM Format Converter | _ description_ |
22- | [ ` bed-to-gff ` ] [ bed-to-gff ] | Coordinate Manipulation | _ description_ |
23- | [ ` composite ` ] [ composite ] | Figure Generation | CLI only! _ description_ |
24- | [ ` dna-shape-bed ` ] [ dna-shape-bed ] | Sequence Analysis | _ description_ |
25- | [ ` dna-shape-fasta ` ] [ dna-shape-fasta ] | Sequence Analysis | _ description_ |
26- | [ ` expand-bed ` ] [ expand-bed ] | Coordinate Manipulation | _ description_ |
27- | [ ` expand-gff ` ] [ expand-gff ] | Coordinate Manipulation | _ description_ |
28- | [ ` fasta-extract ` ] [ fasta-extract ] | Sequence Analysis | _ description_ |
29- | [ ` filter-bed ` ] [ filter-bed ] | Peak Analysis | _ description_ |
30- | [ ` filter-pip-seq ` ] [ filter-pip-seq ] | BAM Manipulation | _ description_ |
31- | [ ` four-color ` ] [ four-color ] | Figure Generation | _ description_ |
32- | [ ` gff-to-bed ` ] [ gff-to-bed ] | Coordinate Manipulation | _ description_ |
33- | [ ` heatmap ` ] [ heatmap ] | Figure Generation | _ description_ |
34- | [ ` md5checksum ` ] [ md5checksum ] | File Utilities | GUI only! _ description_ |
35- | [ ` merge-bam ` ] [ merge-bam ] | BAM Manipulation | GUI only!_ description_ |
36- | [ ` merge-heatmap ` ] [ merge-heatmap ] | Figure Generation | _ description_ |
37- | [ ` pe-stat ` ] [ pe-stat ] | BAM Statistics | _ description_ |
38- | [ ` peak-align-ref ` ] [ peak-align-ref ] | Peak Analysis | _ description_ |
39- | [ ` rand-coord ` ] [ rand-coord ] | Peak Analysis | _ description_ |
40- | [ ` randomize-fasta ` ] [ randomize-fasta ] | Sequence Analysis | _ description_ |
41- | [ ` remove-duplicates ` ] [ remove-duplicates ] | BAM Manipulation | GUI only! _ description_ |
42- | [ ` scale-matrix ` ] [ scale-matrix ] | Read Analysis | _ description_ |
43- | [ ` scaling-factor ` ] [ scaling-factor ] | Read Analysis | _ description_ |
44- | [ ` se-stat ` ] [ se-stat ] | BAM Statistics | _ description_ |
45- | [ ` search-motif ` ] [ search-motif ] | Sequence Analysis | _ description_ |
46- | [ ` signal-dup ` ] [ signal-dup ] | Peak Analysis | _ description_ |
47- | [ ` sort-bam ` ] [ sort-bam ] | BAM Manipulation | GUI only! _ description_ |
48- | [ ` sort-bed ` ] [ sort-bed ] | Coordinate Manipulation | _ description_ |
49- | [ ` sort-gff ` ] [ sort-gff ] | Coordinate Manipulation | _ description_ |
50- | [ ` tag-pileup ` ] [ tag-pileup ] | Read Analysis | _ description_ |
51- | [ ` tile-genome ` ] [ tile-genome ] | Peak Analysis | _ description_ |
52-
53-
54- [ aggregate-data ] :read-analysis/aggregate-data.md
55- [ bam-correlation ] :bam-statistics/bam-correlation.md
56- [ bam-indexer ] :bam-manipulation/bam-indexer.md
57- [ bam-to-bedgraph ] :bam-format-converter/bam-to-bedgraph.md
58- [ bam-to-bed ] :bam-format-converter/bam-to-bed.md
59- [ bam-to-gff ] :bam-format-converter/bam-to-gff.md
60- [ bam-to-scidx ] :bam-format-converter/bam-to-scidx.md
61- [ bed-to-gff ] :coordinate-manipulation/bed-to-gff.md
62- [ composite ] :figure-generation/composite-plot.md
63- [ dna-shape-bed ] :sequence-analysis/dna-shape-bed.md
64- [ dna-shape-fasta ] :sequence-analysis/dna-shape-fasta.md
65- [ expand-bed ] :coordinate-manipulation/expand-bed.md
66- [ expand-gff ] :coordinate-manipulation/expand-gff.md
67- [ fasta-extract ] :sequence-analysis/fasta-extract.md
68- [ filter-bed ] :peak-analysis/filter-bed.md
69- [ filter-pip-seq ] :bam-manipulation/filter-pip-seq.md
70- [ four-color ] :figure-generation/four-color.md
71- [ gff-to-bed ] :coordinate-manipulation/gff-to-bed.md
72- [ heatmap ] :figure-generation/heatmap.md
73- [ md5checksum ] :file-utilities/md5checksum.md
74- [ merge-bam ] :bam-manipulation/merge-bam.md
75- [ merge-heatmap ] :figure-generation/merge-heatmap.md
76- [ pe-stat ] :bam-statistics/pe-stat.md
77- [ peak-align-ref ] :peak-analysis/peak-align-ref.md
78- [ rand-coord ] :peak-analysis/rand-coord.md
79- [ randomize-fasta ] :sequence-analysis/randomize-fasta.md
80- [ remove-duplicates ] :bam-manipulation/remove-duplicates.md
81- [ scale-matrix ] :read-analysis/scale-matrix.md
82- [ scaling-factor ] :read-analysis/scaling-factor.md
83- [ se-stat ] :bam-statistics/se-stat.md
84- [ search-motif ] :sequence-analysis/search-motif.md
85- [ signal-dup ] :peak-analysis/signal-dup.md
86- [ sort-bam ] :bam-manipulation/sort-bam.md
87- [ sort-bed ] :coordinate-manipulation/sort-bed.md
88- [ sort-gff ] :coordinate-manipulation/sort-gff.md
89- [ tag-pileup ] :read-analysis/tag-pileup.md
90- [ tile-genome ] :peak-analysis/tile-genome.md
17+ ### Group codes
18+ | Code | Tool Group | Code | Tool Group |
19+ | ---- | : --------------------- | ---- | : --------------------- |
20+ | ** BF** | BAM Format Converter | ** FU** | File Utilities |
21+ | ** BM** | BAM Manipulation | ** PA** | Peak Analysis |
22+ | ** BS** | BAM Statistics | ** RA** | Read Analysis |
23+ | ** CM** | Coordinate Manipulation | ** SA** | Sequence Analysis |
24+ | ** FG** | Figure Generation |
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