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Eigen 3.4.1 and 5.0.0 available

Status: Open.

#140 In cole-trapnell-lab/cufflinks;

· stefano2734 opened on Oct 17, 2025

Install cufflinks: configure.ac:123: error: AM_INIT_AUTOMAKE expanded multiple times when run ./configure

Status: Open.

#139 In cole-trapnell-lab/cufflinks;

· Gina123e opened on Aug 25, 2024

Unusual behavior of cufflinks when a colon is present in the contig names

Status: Open.

#138 In cole-trapnell-lab/cufflinks;

· sarahfrail opened on Dec 15, 2023

# coverage and -g and -G

Status: Open.

#137 In cole-trapnell-lab/cufflinks;

· BGI2016 opened on Jun 27, 2023

multithreading

Status: Open.

#136 In cole-trapnell-lab/cufflinks;

· denbogdan opened on Jun 20, 2022

cuffdiff error: number of labels must match number of conditions

Status: Open.

#135 In cole-trapnell-lab/cufflinks;

· Giuseppe1995 opened on Apr 14, 2022

Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position

Status: Open.

#134 In cole-trapnell-lab/cufflinks;

· CharlesARoy opened on Oct 29, 2021

Cuffmerge GTF error

Status: Open.

#132 In cole-trapnell-lab/cufflinks;

· nimishakbalan opened on May 19, 2021

cuffmerge

Status: Open.

#131 In cole-trapnell-lab/cufflinks;

· shainijoseph opened on May 13, 2021

Cuffmerge:ValueError: can't have unbuffered text I/O

Status: Open.

#130 In cole-trapnell-lab/cufflinks;

· shainijoseph opened on May 13, 2021

license clarification

Status: Open.

#129 In cole-trapnell-lab/cufflinks;

· rekado opened on Mar 2, 2021

Intron not within scaffold warnings

Status: Open.

#128 In cole-trapnell-lab/cufflinks;

· francicco opened on Jun 27, 2020