foerstner-lab READemption issues

foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data

https://reademption.readthedocs.io

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issues

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Return contribution of genes expression to component of PCA

#66 konrad opened 5 months ago
0
Feature Request: Create z-scores and heatmap plots from z-scores

#65 Tillsa opened 5 months ago
0
[Error] Example for multi-species does not work

#64 elhossary opened 7 months ago
0
Patch for example align

#63 elhossary opened 7 months ago
0
[Feature request] Use NCBI datasets to download input files

#62 elhossary opened 7 months ago
0
Assign libraries for paired end data in the reademption deseq command

#61 termithorbor opened 7 months ago
1
Advantage/disadvantage of build_fragments

#60 termithorbor opened 8 months ago
0
Which alignment mode to use?

#59 termithorbor closed 8 months ago
1
Which normalization from gene_quanti is used for Deseq2?

#58 termithorbor opened 9 months ago
1
Feature request: Create Coverage based on CIGAR string instead of start and end position

#57 Tillsa opened 11 months ago
0
Unusually high memory memory usage with gene_quanti

#56 kmuench opened 1 year ago
15
Constant background value in coverage files

#55 gprezza closed 10 months ago
14
[Clarification] Why are alignments fractional?

#54 kmuench opened 1 year ago
5
Errors and warnings while fragment building

#53 elhossary opened 1 year ago
0
KeyError at alignment stats step

#52 gprezza closed 1 year ago
3
[Bug] File not found in coverage subcommand

#51 elhossary closed 1 year ago
1
[Suggestion] Make fragment building as a separate subcommand

#50 elhossary opened 1 year ago
0
align error "Not a gzipped file"

#49 stefaniamagg closed 1 year ago
2
Automatic determination of file type (fasta or fastq)

#48 Tillsa opened 1 year ago
1
hello .i have error while align using reademption. im sure about the requirements that i have fullfilled .please check the screenshoots and point me the mistake and solution.

#47 AzkaSaleem opened 1 year ago
3
DESeq not working without replicates

#46 mgsrod opened 1 year ago
0
docker container without root

#45 qiyubio opened 2 years ago
2
Conda installation of reademption under /root in Dockerfile results in broken singularity image

#44 anfarr closed 2 years ago
2
coverage -d option for unstranded RNA-Seq library

#43 EthanKhew closed 2 years ago
2
coverage FileNotFoundError (read_alignments_final.json)

#42 gcabebe closed 2 years ago
2
Align subcommand mysteriously takes forever in some runs in ver. 2.0.0

#41 elhossary closed 2 years ago
2
[Feature request] Log

#40 almutwerner closed 2 years ago
1
Error running gene_quanti

#39 jina-leemon closed 2 years ago
3
Metatranscriptome

#38 Thexiyang closed 2 years ago
1
[Feature request] option to filter alignments based on annotation type

#37 elhossary opened 3 years ago
0
Usage problem in align subcommand

#36 elhossary opened 3 years ago
0
[Feature request] Add support for exporting coverage as BigWig

#35 elhossary opened 3 years ago
0
DeSeq visualization gives a future deprecation warning

#34 elhossary closed 2 years ago
0
subcommand align can't recognize pairs of paired end reads

#33 elhossary closed 3 years ago
0
align error (probably segemehl version issue)

#32 npokorzynski closed 2 years ago
8
Update docker image to the latest version

#31 mdphan closed 2 years ago
1
Splitting coverage files if reads for different species aligned together

#30 elhossary closed 2 years ago
0
Getting AttributeError: 'Namespace' object has no attribute 'realign' error

#29 max1c closed 4 years ago
3
Error running align

#28 Rdebar closed 2 years ago
31
Logical issue in coverage min normalization

#27 elhossary opened 4 years ago
0
Mapping unaligned reads with lack should be removed

#26 elhossary closed 2 years ago
0
Installation documentation of DeSeq2

#25 elhossary closed 2 years ago
0
installation issue

#24 Haley-Wami closed 4 years ago
3
align error with example data.

#23 Jomagrax closed 4 years ago
11
Incorrect documentation of a parameter in subcommand "Coverage"

#22 elhossary closed 2 years ago
0
Error in vizual align with paired end libraries

#21 elhossary closed 2 years ago
0
Add subcommand to check gff files

#20 konrad opened 5 years ago
0
Generate counting of unmapped reads directly from the bam file

#19 konrad opened 5 years ago
0
Fix failing test and extend CI running of tests

#18 konrad closed 2 years ago
0
Create conda package and add it to bioconda

#17 konrad closed 2 years ago
0