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pachterlab/sleuth
sleuth_prep fail, read_kallisto , is(path, "character") is not TRUE

new env conda install --channel bioconda r-sleuth Total: 245.0 MB r-sleuth-0.30.0 python-3.11.5 r-base-3.6.1 ... R library( sleuth ) samples = c( CK1 , CK2 , CK3 , Y22_3HM1 , Y22_3HM2 , Y22_3HM3 ) s2c ...
  • DingJingZhi
  • 2
  • Opened 
    on Dec 12, 2024
  • #286

pachterlab/sleuth
Simple Error in measurement_error.R

Hi -- I found what I think is a pretty simple error in measurement_error.R. In the following block of code, $lwr is incorrectly written into upr: if ( upr %in% names(extra_opts)) { upr - extra_opts$lwr ...
  • pcp2117
  • Opened 
    on Nov 19, 2023
  • #284

pachterlab/sleuth
Error in model_exists(obj, null_model) : model 'reduced' not found

Dears authors, I also have problems when I run the following codes. Would you please help me sloving it? Thanks! `s2c sample condition   SRR493366 Scramble SRR493367 Scramble SRR493368 Scramble SRR493369 ...
  • ljz3216
  • Opened 
    on Oct 5, 2023
  • #283

pachterlab/sleuth
TPM values depend on Combination

Using sleuth I can calculate the TPM-Value of a gene in a Sample (sleuth_prep followed by sleuth_to_matrix). Now if I have 6 samples (6 abundance tables from Kallisto) with two belonging to on of the ...
  • keksundso
  • 2
  • Opened 
    on Sep 19, 2023
  • #282

pachterlab/sleuth
no replications

hello, I d like to know whether sleuth would use for experimental analysis with no replications?
  • xingjianfeng100
  • Opened 
    on Sep 7, 2023
  • #281

pachterlab/sleuth
Issue with reading kallisto results

Hello, Thank you advance for your help. I have run kallisto to quantify a series of RNA seq experiments and I was going to analyze the results with sleuth. Never tried this before and I was following the ...
  • rmsalatino
  • Opened 
    on Jun 20, 2023
  • #280

pachterlab/sleuth
Issue with simpleLoess

Hello! I am enjoyed on the abilities the sleuth provides on RNA-Seq data analysis. So I try to use it in my current project. I have a large dataset, where from I am interested in looking the DE for 15 ...
  • asan-emirsaleh
  • 4
  • Opened 
    on Jun 7, 2023
  • #278

pachterlab/sleuth
Testing for interactions

I am currently working on DGE (liver; males and females) data from a lab experiment where I have reared stickleback in contrasting temperatures and diets. Is there a way to test for interactions using ...
  • AlessandraSchnider
  • Opened 
    on Feb 14, 2023
  • #277

pachterlab/sleuth
select_() was deprecated in dplyr 0.7.0.

ℹ Please use spread() instead. ℹ The deprecated feature was likely used in the sleuth package. Please report the issue at https://github.com/pachterlab/sleuth/issues .
  • AlexGaithuma
  • 1
  • Opened 
    on Jan 17, 2023
  • #276

pachterlab/sleuth
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file.

Hello, I am having the same problem: so - sleuth_prep(s2c, ~ condition) reading in kallisto results ..Error in H5Fopen(file, H5F_ACC_RDONLY ) : HDF5. File accessability. Unable to open file. SessionInfo() ...
  • martalopes5234
  • 2
  • Opened 
    on Sep 15, 2022
  • #274
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