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pachterlab
/
seqspec
machine-readable file format for genomic library sequence and structure
MIT License
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predefined `sequence_protocol`
#49
sbooeshaghi
opened
1 month ago
0
seqspec split error
#48
RaiRuhi
closed
1 month ago
1
using region.max_len for format and check is a problem for nanopore reads
#47
detrout
closed
1 month ago
1
Feature request: grouping of sequencing runs
#46
visze
closed
3 weeks ago
2
source file for pypi
#45
visze
opened
2 months ago
1
With a seqspec that has only one modality it seems like the library png plot is too short.
#44
detrout
opened
2 months ago
0
getting an unexpected keyword argument error in seqspec init
#43
bdoughty
closed
3 months ago
2
- fix chromap format
#42
sidwekhande
closed
3 months ago
1
Revert " - fix chromap format"
#41
sbooeshaghi
closed
3 months ago
0
index string should take into account strand information
#40
sidwekhande
closed
1 month ago
3
Deterministic fastq filename deduplication, use a previously downloaded barcode file, add a longer error message and fixing unit tests.
#39
detrout
closed
3 months ago
1
- fix chromap format
#38
sidwekhande
closed
3 months ago
2
Fixes
#37
detrout
closed
4 months ago
0
format chromap potentially is not deterministic as python set() does not have a guaranteed order,
#36
detrout
closed
3 months ago
1
Update SPECIFICATION.md to match JSON schema
#35
devin-ai-integration[bot]
closed
4 months ago
0
Comprehensive Documentation and Updated Tests for Seqspec
#34
devin-ai-integration[bot]
closed
4 months ago
1
seqspec enhacements (addition of library specification + read specification)
#33
sbooeshaghi
closed
4 months ago
1
Libspec local caching
#32
detrout
closed
4 months ago
2
remote onlist download with the kallisto multiple lists onlist format
#31
detrout
closed
6 months ago
1
Improve tests, add downloading barcodes, and a new barcode list format.
#30
detrout
closed
6 months ago
0
we need a region_type to represent gRNA/sgRNA_targets
#29
RaiRuhi
closed
4 months ago
1
Please make an initial release
#28
johanneskoester
closed
9 months ago
3
getting not unique across all regions error but region_id is unique
#27
visze
closed
4 months ago
4
DNA for modalities
#26
visze
closed
10 months ago
3
10x-RNA-v3 barcode file
#25
b-coli
closed
10 months ago
3
missing support for custom read primer definition
#24
bnovak32
closed
10 months ago
6
add requests to requirements
#23
chooliu
closed
10 months ago
1
snmCT-seq assay spec
#22
chooliu
closed
10 months ago
1
sn-m3C-seq assay spec
#21
chooliu
closed
10 months ago
1
add "requests" package as dependency?
#20
chooliu
closed
10 months ago
0
expand sequence in schema.json for IUPAC nucleotides
#19
chooliu
closed
11 months ago
1
Make to_dict and to_JSON generate dictionaries with keys in the same order
#18
detrout
closed
1 year ago
0
read seqspec from URI
#17
hitz
closed
10 months ago
9
Added RNA-ATAC-MULTI-seq for IGVF upload
#16
Jacobog02
closed
1 year ago
1
speck check is allowing different region_type
#15
emattei
closed
1 year ago
1
Linker is not a region_type
#14
emattei
closed
1 year ago
1
Print not working on Windows
#13
emattei
closed
10 months ago
3
added specs for ISSAAC-seq, PIP-seq V2 and PIP-seq V3
#12
dbrg77
closed
1 year ago
8
PIP-seq
#11
lakigigar
closed
1 year ago
5
Jsonschema requirements
#10
detrout
closed
1 year ago
1
seqspec for parse wt-mega v2 kit
#9
detrout
closed
1 year ago
12
Sequencing data repositories which accept seqspec?
#8
photocyte
closed
1 year ago
2
to_dict() should return the order parameter.
#7
detrout
closed
1 year ago
2
Draft4Validator.iter_errors is expecting a dictionary
#6
detrout
closed
1 year ago
1
package uses, but does list jsonschema in requirements.
#5
detrout
closed
1 year ago
1
Testing core object types
#4
detrout
closed
1 year ago
4
Improvements
#3
sbooeshaghi
opened
1 year ago
0
Broad share spec
#2
emattei
closed
1 year ago
4
added assay sci-RNA-seq3
#1
meichenfang
closed
1 year ago
0