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Add an option to output the transcript/gene counts for all the available options for a single run

enhancementNew feature or requestNew feature or request

Status: Open.

#339 In ablab/IsoQuant;

· mpage21 opened on Sep 11, 2025

Parameters for the quantification step

enhancementNew feature or requestNew feature or request

Status: Open.

#338 In ablab/IsoQuant;

· hyeon9 opened on Sep 8, 2025

Difference between using a merged BAM vs. a YAML file with replicates

questionFurther information is requestedFurther information is requested

Status: Open.

#336 In ablab/IsoQuant;

· marco-cominelli01 opened on Sep 5, 2025

issue with single cell mode in 3.6.0-sc

Status: Open.

#334 In ablab/IsoQuant;

· SuiYue-2308 opened on Aug 21, 2025

Using IsoQuant counts with DESeq2?

questionFurther information is requestedFurther information is requested

Status: Open.

#331 In ablab/IsoQuant;

· gaoxiangcao opened on Aug 7, 2025

The strand of the reads in the read_assignments is not same with the strand aligned to the genome

Status: Open.

#329 In ablab/IsoQuant;

· creaturemoon opened on Aug 4, 2025

minor_exon_elongation cutoff

Status: Open.

#325 In ablab/IsoQuant;

· lyj95618 opened on Jul 30, 2025

error in running isoquant single cell mode

Status: Open.

#324 In ablab/IsoQuant;

· sofiedemeyer opened on Jul 30, 2025

read assignment for every transcript

questionFurther information is requestedFurther information is requested

Status: Open.

#323 In ablab/IsoQuant;

· xhuashen opened on Jul 26, 2025

Single nuclei data quantification with Isoquant

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#322 In ablab/IsoQuant;

· ADelgadoT opened on Jul 22, 2025

IsoQuant fails with BrokenProcessPool and OOM killed during collect_reads

Status: Open.

#320 In ablab/IsoQuant;

· AaronMask opened on Jul 11, 2025

SQANTI-like Output Header and Novel Isoforms

bugSomething isn't workingSomething isn't working

questionFurther information is requestedFurther information is requested

weird resultsSomething looks odd in the resulting filesSomething looks odd in the resulting files

Status: Open.

#318 In ablab/IsoQuant;

· GaryWang7 opened on Jun 20, 2025