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databio
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gtars
Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.
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Refactor bam to bw workflow
#47
donaldcampbelljr
opened
1 week ago
0
cargo build causes error on newest branch dev_bam_bedgraph_bigtools
#46
ClaudeHu
closed
3 weeks ago
3
IGD Search is returning 0 hits in some test cases
#45
donaldcampbelljr
opened
3 weeks ago
2
attempt txt input update
#44
sanghoonio
opened
3 weeks ago
12
Missing start=setting line in the core file generated by uniwig
#43
saanikat
opened
3 weeks ago
3
Double-tokenizing a `RegionSet` will result in no tokens
#42
nleroy917
opened
1 month ago
1
Dev bed graph compress counts
#41
donaldcampbelljr
closed
1 month ago
0
Add bam support for counting intervals
#40
donaldcampbelljr
opened
1 month ago
0
Add basic R bindings
#39
nleroy917
opened
1 month ago
1
Add fragment file region scoring matrix creation
#38
nleroy917
opened
1 month ago
0
Add converting files to bigWig
#37
donaldcampbelljr
closed
1 month ago
1
Dev narrow peak scoring
#36
donaldcampbelljr
closed
1 month ago
6
Add pseudobulking code
#35
nleroy917
closed
1 month ago
0
Count based on narrowPeak score
#34
donaldcampbelljr
opened
1 month ago
0
Rename uniwig
#33
donaldcampbelljr
opened
1 month ago
0
Bypass filesystem with uniwig using fifos
#32
nsheff
opened
1 month ago
0
Performance improvements for writing to .wig files
#31
donaldcampbelljr
closed
1 month ago
0
Add ability for rust uniwig to create output files from input .bam files
#30
donaldcampbelljr
opened
1 month ago
1
Error from uniwig regarding mismatched chromosomes in BED and .sizes files
#29
ClaudeHu
closed
3 months ago
7
Implement IGD
#28
nleroy917
opened
3 months ago
3
Hierarchical tokenizers
#27
nleroy917
closed
4 months ago
1
Rename repository to `gtars`
#26
nleroy917
closed
5 months ago
0
Hierarchical universes and a tokenizer config
#25
nleroy917
opened
5 months ago
0
Release `v0.0.13` -- Add fragment file tokenizer
#24
nleroy917
closed
5 months ago
1
Implement a basic fragment file tokenizer
#23
nleroy917
closed
6 months ago
0
Fix pything bindings tokenization performance issues
#22
nleroy917
closed
6 months ago
0
Python bindings memory leak and performance issues
#21
nleroy917
closed
6 months ago
1
PanicException during tokenization
#20
ClaudeHu
closed
3 months ago
9
Tokenize all the things - genomic omni-model
#19
nleroy917
opened
6 months ago
0
Python bindings wont build for linux `aarch64`
#18
nleroy917
closed
5 months ago
9
Soft tokenizer
#17
nleroy917
closed
6 months ago
0
Release `v0.0.12`
#16
nleroy917
closed
6 months ago
2
Convert to workspace
#15
nleroy917
closed
3 months ago
1
Implement an `AnnData` tokenizer
#14
nleroy917
opened
7 months ago
0
Better tokenization API
#13
nleroy917
closed
7 months ago
1
Implement a `return_tensors="pt"` function for the Tokenizers
#12
nleroy917
closed
3 months ago
1
Dev uniwig
#11
donaldcampbelljr
closed
3 months ago
31
Inconsistent region numbers
#10
gtzheng
opened
9 months ago
4
Dev igd
#9
donaldcampbelljr
closed
1 month ago
2
add AIList and bindings
#8
edward9065
closed
11 months ago
0
Implement a soft tokenizer
#7
nleroy917
opened
11 months ago
1
Merge master changes into dev branch
#6
edward9065
closed
11 months ago
0
The `TokenizedRegionSet` needs to have a `to_ids()` function on it
#5
nleroy917
closed
3 months ago
2
Tokenizers should sort universe files before creating `region_to_id` maps
#4
nleroy917
opened
12 months ago
0
Core utilities
#3
nleroy917
closed
12 months ago
6
Implement some core utils
#2
nleroy917
closed
3 months ago
1
Implement `uniwig`
#1
nleroy917
opened
1 year ago
13