thelovelab tximport issues

thelovelab / tximport

Transcript quantification import for modular pipelines

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issues

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tximport of kallisto h5s generated with multiple threads is not deterministic

#58 ning-y closed 5 months ago
1
rename piscem-infer to piscem in field

#57 rob-p closed 11 months ago
0
Add initial support for `piscem-infer`

#56 rob-p closed 11 months ago
0
tximport of feature counts?

#55 marwa38 closed 1 year ago
1
Different length and counts depending on the number of loaded samples

#54 FlorianRocher closed 1 year ago
1
Dealing with multispecies using tximport

#53 FlorianRocher closed 1 year ago
4
import using tximport for the rsem count table to get integers?

#52 marwa38 closed 1 year ago
3
error in 1:nrow(m): argument of length 0

#51 SylwiaPiatkowska closed 1 year ago
1
make filterByExpr use design information

#50 ATpoint closed 2 years ago
1
Which measure to use for gene Fold change analysis between pre- and post-treatment samples and for gene comparison within a sample

#49 mpunta closed 2 years ago
1
added check for timezone and Olson database

#48 ATpoint closed 3 years ago
1
Tximport issue with new R version

#47 alexandregmartini closed 3 years ago
2
Read in files in parallel

#46 grst closed 3 years ago
4
edgeR::cpm

#45 ATpoint closed 3 years ago
2
Returns TPM when abundanceCol is set to any value for type='rsem'

#44 csmith-pact closed 3 years ago
1
Recomended count scaling method for DTU analysis

#43 kvittingseerup closed 4 years ago
2
Import processed data

#42 koenvandenberge closed 4 years ago
3
cann't import kallisto abundance.h5/.tsv

#41 Ci-TJ closed 4 years ago
4
`ignoreAfterBar` not used if `txOut=TRUE`

#40 csoneson closed 3 years ago
5
lose transcript names for salmon inferential replicates

#39 cindywen96 closed 4 years ago
0
ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no"

#38 karl616 closed 4 years ago
1
Add option to import only whitelisted barcodes from alevin

#37 csoneson closed 4 years ago
2
Missing release tags

#36 smoe closed 5 years ago
1
Move Alevin import code to C++

#35 mikelove closed 5 years ago
3
Outdated vignette?

#34 TobiTekath closed 5 years ago
1
Error in importing RSEM gene level result files

#33 Duanzpwt closed 5 years ago
0
can't read alevin output from salmon 0.14.0

#32 alexvpickering closed 5 years ago
8
Error against the result of salmon with option --numBootstraps

#31 kokitsuyuzaki closed 5 years ago
1
Fix for Salmon 0.14 num_targets -> num_valid_targets issue.

#30 roryk closed 5 years ago
10
Importing transcript abundance datasets generated with Salmon 0.14.0

#29 edoardobertolini closed 5 years ago
5
Minor edits to edgeR part of the vignette.

#28 LTLA closed 5 years ago
3
Error in H5Fopen

#27 uso2015 closed 5 years ago
1
Transcript expression collapsing to gene-level expression

#26 beginner984 closed 5 years ago
3
sparse matrix support?

#25 koenvandenberge closed 5 years ago
22
Idea: Supporting alevin output

#24 PeteHaitch closed 5 years ago
10
Feature Idea : Derive abundance from inferential replicates

#23 rob-p closed 6 years ago
2
filtering lowly expreed genes after or before normalization ?

#22 atasub closed 6 years ago
1
Check for existence of abundance.h5 before checking for rhdf5?

#21 csoneson closed 6 years ago
1
Enabling reading from cloud storage

#20 tomsing1 closed 6 years ago
3
Please read this before submitting an issue or PR

#19 mikelove opened 6 years ago
0
Add kallisto HDF5 import

#18 andrewparkermorgan closed 6 years ago
2
Error: all(file.exists(files)) is not TRUE

#17 cartal closed 7 years ago
1
Typo in instructions for using ensembldb

#16 PeteHaitch closed 7 years ago
0
Unexpected behavior when processing RSEM transcript level files

#15 ecoenen closed 8 years ago
1
Allow missing-ness in individual transcriptomes

#14 mdshw5 closed 8 years ago
2
rename argument: gene2tx => tx2gene

#13 mikelove closed 8 years ago
0
feature request: modularize gene-level summarization when txOut=TRUE

#12 stephenturner closed 8 years ago
2
make it easier to read in rsem tx-level ests

#11 mikelove closed 7 years ago
1
better warning if no tx2gene provided

#10 mikelove closed 8 years ago
0
Support for new sailfish and salmon formats

#9 rob-p closed 8 years ago
2