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Hello LEfSe users! 

Please direct all future questions about LEfSe to our new Discourse forum:
https://forum.biobakery.org/
This forum can be viewed by anyone, but you will need to ***create an account to post a new question***. 
This Google Group is now set as "read only": You may continue to browse existing message threads within the Group, but new messages sent to the Group will bounce back as "undeliverable".

By migrating all questions and answers to a centralized forum, we aim to both increase their visibility across the bioBakery user community in addition to improving response times.
Sincerely,
The bioBakery Support Team

ReplyForward

0 selected

12/4/19

Google Groups Depcrecation

The Google group list serve will be replaced by our bioBakery Discourse site on [23rd Dec, 2019]. The

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Google Groups Depcrecation

The Google group list serve will be replaced by our bioBakery Discourse site on [23rd Dec, 2019]. The

12/4/19

Renan Soares, … jfg6

10/7/16

Does an OTU interfere in another?

Dear Nicola, Can I suggest this post (or one similar, eg a quick FAQ) is stickied to the top of the

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Does an OTU interfere in another?

Dear Nicola, Can I suggest this post (or one similar, eg a quick FAQ) is stickied to the top of the

10/7/16

1/21/20

New LEfSe Forum !

Hello LEfSe users! Please direct all future questions about LEfSe to our new Discourse forum: https:/

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New LEfSe Forum !

Hello LEfSe users! Please direct all future questions about LEfSe to our new Discourse forum: https:/

1/21/20

Amir alipour yengejeh, Eric Franzosa2

12/19/19

The Group is inactive

Support for all bioBakery tools is being migrated to: https://forum.biobakery.org/. Thanks, Eric On

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The Group is inactive

Support for all bioBakery tools is being migrated to: https://forum.biobakery.org/. Thanks, Eric On

12/19/19

12/19/19

LefSe: what happens if no subclass

I posted this on the new biobakery help forum, but received no replies so I'm duplicating here

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LefSe: what happens if no subclass

I posted this on the new biobakery help forum, but received no replies so I'm duplicating here

12/19/19

Amir alipour yengejeh

12/19/19

no consistency between plot and table

Hello, I am using Lefse commands on biobakery. However, my problem is that when I generate histogram

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no consistency between plot and table

Hello, I am using Lefse commands on biobakery. However, my problem is that when I generate histogram

12/19/19

Amir alipour yengejeh

12/17/19

Hello all, I am a new user of Lefse, and I have got this group very wonderful. I am using LEfSe on

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Hello all, I am a new user of Lefse, and I have got this group very wonderful. I am using LEfSe on

12/17/19

Levesque, Nicole M., Hanna Berggrem2

12/9/19

FW: LEfSe output: number of features in the output highly exceed the number in the input data

Dear Safaa, We experienced the same problem, did you find any explanation/solution for this? Best

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FW: LEfSe output: number of features in the output highly exceed the number in the input data

Dear Safaa, We experienced the same problem, did you find any explanation/solution for this? Best

12/9/19

Curtis Huttenhower

12/2/19

Re: Questions about LEfSe

Hi Luc - thanks for getting in touch; I've CCed in the LEfSe users group here, and especially

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Re: Questions about LEfSe

Hi Luc - thanks for getting in touch; I've CCed in the LEfSe users group here, and especially

12/2/19

11/18/19

Suggestion: Option for Correcting for Multiple Comparisons

Dear LefSe Developers, Thanks you for availing LefSe to the scientific community. Mine is just a

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Suggestion: Option for Correcting for Multiple Comparisons

Dear LefSe Developers, Thanks you for availing LefSe to the scientific community. Mine is just a

11/18/19

Jose Antonio Morillo Perez

10/3/19

LefSe with absolute abundances?

Dear colleagues, I am a environmental microbiologists working at CSIC (Spain). First, I would like to

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LefSe with absolute abundances?

Dear colleagues, I am a environmental microbiologists working at CSIC (Spain). First, I would like to

10/3/19

Akriti Singh, Jérémie Auger2

9/19/19

LEfSe LDA plot issue

What do you mean by "missing taxa"? The lines that only read " __ " ? Those are

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LEfSe LDA plot issue

What do you mean by "missing taxa"? The lines that only read " __ " ? Those are

9/19/19

Esther Merlini, Jérémie Auger4

9/19/19

problems with cladogram plot

What do you upload to LefSe? More than one table? I never uploaded my 16S bacterial DB to LefSe. The

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problems with cladogram plot

What do you upload to LefSe? More than one table? I never uploaded my 16S bacterial DB to LefSe. The

9/19/19

Mohamad Khairil

9/12/19

Syntax error while executing "run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res"

Good day. I am Mohamad Khairil Radzali, a postgraduate student from Universiti = Putra Malaysia,

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Syntax error while executing "run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res"

Good day. I am Mohamad Khairil Radzali, a postgraduate student from Universiti = Putra Malaysia,

9/12/19

Levesque, Nicole M.

9/11/19

FW: Help to create a Plot Cladogram

Hello – this person may have already been helped but just unearthed this in my inbox and wanted to

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FW: Help to create a Plot Cladogram

Hello – this person may have already been helped but just unearthed this in my inbox and wanted to

9/11/19

Wellinton Muniz, Jérémie Auger6

9/6/19

Help with LEfSE

So, did you get it working? If not, I have a bit of spare time today, send table, I'll format it

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Help with LEfSE

So, did you get it working? If not, I have a bit of spare time today, send table, I'll format it

9/6/19

Seweryn Bialasiewicz

7/17/19

Binary measures as OTU values - appropriate for LEfSe?

Hello all, I was wondering if anyone could comment on the appropriateness of using LEfSe on a binary

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Binary measures as OTU values - appropriate for LEfSe?

Hello all, I was wondering if anyone could comment on the appropriateness of using LEfSe on a binary

7/17/19

Alla Kubant, … George Weingart3

7/5/19

LEfSe Galaxy Server Down?

Galaxy is up again We incurred a server problem and it has been solved Best regards, George Weingart

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LEfSe Galaxy Server Down?

Galaxy is up again We incurred a server problem and it has been solved Best regards, George Weingart

7/5/19

Levesque, Nicole M.

6/27/19

FW: MGH-Galaxy is not working

Good morning, Can someone please reach out to help Kanakaraju? Thanks, Nicole From: Kaliannan,

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FW: MGH-Galaxy is not working

Good morning, Can someone please reach out to help Kanakaraju? Thanks, Nicole From: Kaliannan,

6/27/19

Levesque, Nicole M.

6/6/19

FW: Information related to Lefse

Good morning – can someone please reach out to Debarghya? Thanks, Nicole From: Debarghya Nandi <

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FW: Information related to Lefse

Good morning – can someone please reach out to Debarghya? Thanks, Nicole From: Debarghya Nandi <

6/6/19

5/21/19

Dear Lefse developers, Thanks for a great tool! I really like the visualisation as well. I have a few

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Dear Lefse developers, Thanks for a great tool! I really like the visualisation as well. I have a few

5/21/19

Clémence Landreau

5/13/19

Understanding LEfSe results table

Good afternoon, I am a french student working on microbiota data in Crohn's disease. I am working

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Understanding LEfSe results table

Good afternoon, I am a french student working on microbiota data in Crohn's disease. I am working

5/13/19

Levesque, Nicole M.

4/26/19

FW: Fw:Account quotas

Hi there, I'm not sure but I think this person is trying to use Lefse? Thanks Nicole -----

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FW: Fw:Account quotas

Hi there, I'm not sure but I think this person is trying to use Lefse? Thanks Nicole -----

4/26/19

Levesque, Nicole M.

4/25/19

FW: LEfSe Issue

Good afternoon, Please see below. Thanks, Nicole From: Karthik Yarlagadda <karth...@gmail.com

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FW: LEfSe Issue

Good afternoon, Please see below. Thanks, Nicole From: Karthik Yarlagadda <karth...@gmail.com

4/25/19

4/22/19

lefse and repeated measures data

Hi LEfSe forum Could someone please clarify for me how/if lefse accounts for correlation between

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lefse and repeated measures data

Hi LEfSe forum Could someone please clarify for me how/if lefse accounts for correlation between

4/22/19

4/14/19

PICRUSt2 output to LEfSe input

Dear All, I would like to know if there is any tutorial about how to format the PICRUSt2 output to

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PICRUSt2 output to LEfSe input

Dear All, I would like to know if there is any tutorial about how to format the PICRUSt2 output to

4/14/19

jfg, … am...@usc.edu6

3/20/19

homonymous OTUs mask LDA Effect Size

Hi Jfg and Nicola, I have tried to understand this by reading the different conversations in the

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homonymous OTUs mask LDA Effect Size

Hi Jfg and Nicola, I have tried to understand this by reading the different conversations in the

3/20/19

Levesque, Nicole M.

3/8/19

Can someone please reach out to Tonia? Thank you, Nicole From: Tonia De Bellis <tdebellis@

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Can someone please reach out to Tonia? Thank you, Nicole From: Tonia De Bellis <tdebellis@

3/8/19

Liam Shaw, … jian wang5

3/5/19

LEfSe output file

Hi Nicola, I am new to LEfSe and having questions regarding to the output file for the LDA effect

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LEfSe output file

Hi Nicola, I am new to LEfSe and having questions regarding to the output file for the LDA effect

3/5/19

Jennifer Huang, … PaulineV7

3/4/19

Import error: No modules named rpy2.robjects

Hi everyone, This is quite an old post but I didn't want to open a new one since I am having the

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Import error: No modules named rpy2.robjects

Hi everyone, This is quite an old post but I didn't want to open a new one since I am having the

3/4/19

Jonathan Greenberg

2/22/19

Changing Alpha value for ANOVA giving different features

Hello, I apologize for having a second topic, but in addition to my previous question, I have run

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Changing Alpha value for ANOVA giving different features

Hello, I apologize for having a second topic, but in addition to my previous question, I have run

2/22/19

lina....@gmail.com, Jonathan Greenberg2

2/19/19

Setting alpha cutoffs for KW and Wilcoxon tests

Interesting question, I am curious if this was ever answered. On Monday, December 14, 2015 at 2:09:21

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Setting alpha cutoffs for KW and Wilcoxon tests

Interesting question, I am curious if this was ever answered. On Monday, December 14, 2015 at 2:09:21

2/19/19

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