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griffithlab
/
regtools
Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
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Regtools junction extract: strandness detection malfunction
#197
santataRU
opened
1 month ago
0
fix: junctions extractor count overlapping read pairs once
#196
TimD1
opened
2 months ago
3
feat: added per-read anchor requirement to junction extract
#195
TimD1
opened
2 months ago
0
feat: added per-read flag and map quality filtering
#194
TimD1
opened
2 months ago
0
fix: min_intron_length initialization in JunctionsExtractor
#193
TimD1
opened
2 months ago
0
fix: CMake build errors on Mac resolved
#192
TimD1
opened
2 months ago
0
Resolve CMake build errors on Mac
#191
TimD1
closed
2 months ago
0
Issues with Regtools Statistical Analysis Workflow
#190
mguaita
opened
2 months ago
0
feat: Allow read filtering based on mapping quality to `junctions extract`
#189
yfarjoun
opened
4 months ago
0
Bug: min_intron_length_ accidentally initialized from anchor (not intron) length parameter
#188
TimD1
opened
4 months ago
0
bug report: junction extract tool should not count overlapping reads as double support for a junction
#187
yfarjoun
opened
5 months ago
0
Feature request: add per-read anchor requirement to `junction extract` tool
#186
yfarjoun
opened
5 months ago
0
Unrecognized strandness argument!
#185
hsymoon
opened
6 months ago
1
KeyError: 'score' problem
#184
CuteGold0407
opened
7 months ago
0
Feature request
#183
Mohamed-HAMICI
opened
8 months ago
1
Question about single cell regtools junctions extract.
#182
xiaohe0404
opened
8 months ago
0
Splice junctions are delayed by one position at the 5' side
#181
bkffadia
opened
11 months ago
0
Building error
#180
aravindpad
opened
11 months ago
2
Test data for regtools cannot be found!
#179
Eteleeb
opened
1 year ago
0
Questions about compare_junctions_hist_v2.R
#178
R-Najjar
opened
1 year ago
3
unable to open bam file
#177
smurph50
closed
1 year ago
2
installation problem
#176
smurph50
opened
1 year ago
4
Run Time
#175
gnatowskie
closed
1 year ago
0
The -b option of "junctions extract" doesn't work
#174
NaotoKubota
closed
4 months ago
1
cannot detect strandedness from cellranger bam file
#173
ckong1806
closed
1 year ago
3
Multiple input BAM
#172
alexcorm
opened
1 year ago
0
add updated dockerfile which installs python libs
#171
kcotto
closed
1 year ago
1
New statistics script to allow for different variant grouping modes
#170
kcotto
closed
1 year ago
1
update workflow page with more details
#169
kcotto
closed
1 year ago
1
update docs
#168
kcotto
closed
1 year ago
1
update docs
#167
kcotto
closed
1 year ago
1
invalid strand values after running junctions extract
#166
Vishvak2000
opened
2 years ago
1
Junction extract: different junction start/end sites detected using short and long reads
#165
ErminZ
opened
2 years ago
1
regtools 0.6.0
#164
marie-mille
closed
2 years ago
1
Incorporate single cell changes
#163
kcotto
closed
2 years ago
1
update files
#162
kcotto
closed
2 years ago
0
Edit docs
#161
kcotto
closed
2 years ago
1
(never mind)
#160
csjohnson23
closed
2 years ago
0
cis-splice-effects identify junction boundaries differ it TSV and BED output
#159
jje42
closed
2 years ago
2
for long-read RNA-seq data
#158
changeran
closed
2 years ago
0
install problem in make file
#157
changeran
closed
2 years ago
1
rmath.dir build error
#156
kanefos
closed
2 years ago
2
CRAM file support
#155
BEFH
closed
1 year ago
1
Remove `.DS_Store`; add `.DS_Store` to `.gitignore`
#154
sehilyi
closed
3 years ago
2
Comments/problems noticed while getting Example workflow to run
#153
toddajohnson
opened
3 years ago
1
add variants.sh script
#152
kcotto
closed
3 years ago
1
Example workflow mentions variants.sh, but it could not be found
#151
toddajohnson
opened
3 years ago
3
why am I getting an "Error parsing inputs!(2)" error message when using regtools junctions extract?
#150
skalava23
closed
1 year ago
2
Junction annotation questions
#149
yanwang271
opened
3 years ago
2
fix dockerfile to work correctly
#148
kcotto
closed
3 years ago
1
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