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pachterlab
/
sleuth
Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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[Suggestion] When possible, output beta even when performing LRT
#185
zefrieira
opened
6 years ago
0
Allow for filter functions that operate on the whole matrix rather than by row
#184
byoo
opened
6 years ago
6
beta values do not appear in Wald test results when the analysis is performed with gene level aggregation
#183
kalyanuw
closed
6 years ago
1
Improved sanity checks and testing
#182
warrenmcg
closed
6 years ago
1
Typo in sleuth.R in line 832
#181
pkerbs
closed
6 years ago
2
bug in `summary.sleuth`
#180
pimentel
closed
6 years ago
0
Version 0.30.0
#179
pimentel
closed
6 years ago
0
Getting Zero DEGs (but there are definitely some )
#178
seyfim
opened
6 years ago
2
NA/NaN/Inf in foreign function call (arg 11)
#177
sosug32
closed
6 years ago
2
read_kallisto_h5 detects non-unique target_ids
#176
channsoden
closed
6 years ago
6
HDF5 files not being read properly (hdf5 lib incompatibility, or base R and rhdf5 clash?)
#175
channsoden
opened
6 years ago
39
sleuth_to_matrix returns columns in random order
#174
vegardny
closed
6 years ago
1
NA in likelihood ratio test with small number of transcripts
#173
winni2k
opened
6 years ago
6
added link to new walkthrough
#172
lynnyi
closed
6 years ago
3
Broken Link to Test Data in Vignette
#171
pdellorusso
opened
6 years ago
0
add R documentation back to github site under the manual tab
#170
warrenmcg
closed
6 years ago
1
Error in bs_mat[, which_ids]
#169
Rdroit
closed
6 years ago
5
sleuth "Advanced options"
#168
warrenmcg
closed
6 years ago
2
Release version for p-value aggregation features
#167
johnomics
closed
6 years ago
2
Current sleuth_prep procedure doesn't record number of bootstraps present
#166
warrenmcg
closed
6 years ago
1
Sleuth tpm and sleuth live
#165
bioinfo-dirty-jobs
opened
6 years ago
2
'aggregation column' not working
#164
sklasfeld
opened
6 years ago
6
Patch: bugs in sleuth_results & other miscellaneous fixes
#163
warrenmcg
closed
6 years ago
1
> sleuth_live(so) 'browser' must be a non-empty character string
#162
bioinfo-dirty-jobs
opened
6 years ago
2
Kallisto - How to change number of bootstraps?
#161
ScottSchumacker
closed
6 years ago
2
Fix behavior of sleuth_results when gene_mode is TRUE (and error reporting)
#160
warrenmcg
closed
6 years ago
1
Shiny and Plot Fixes / Enhancements
#159
warrenmcg
closed
6 years ago
1
`sleuth_live` will not run if sleuth_wt is run before sleuth_lrt
#158
pimentel
closed
6 years ago
1
Quick Patch: UseMethod typo
#157
warrenmcg
closed
6 years ago
1
Contrast type function in Sleuth
#156
JoanaBSilvestre
closed
6 years ago
5
Sample data download link in "Getting started" walkthrough is dead
#155
lukauskas
opened
6 years ago
3
Trouble with the Sleuth_wt function
#154
ScottSchumacker
closed
6 years ago
6
data.table error in devel branch
#153
Retr0
opened
6 years ago
6
sleuth problem duplicate
#152
bioinfo-dirty-jobs
opened
6 years ago
3
unused argument in `(total = .(total = sum(est_counts)))` for new check zero code
#151
warrenmcg
closed
6 years ago
2
Update `write_kallisto_hdf5` function and add ability to subset kallisto object (address #131)
#150
warrenmcg
closed
6 years ago
1
Error while working on sleuth in Linux
#149
vasanthmandla
closed
6 years ago
4
P-value aggregate
#148
pimentel
closed
6 years ago
0
reordering factors to correct the fold change
#147
DrHeisenberg89
closed
7 years ago
1
problem with target_mapping
#146
DrHeisenberg89
closed
7 years ago
1
extend sleuth to model TPMs
#145
warrenmcg
closed
6 years ago
1
Fixes to various miscellaneous issues (#73, #84, #97, #122, #135, #142)
#144
warrenmcg
closed
7 years ago
2
Improvements to shiny and plot functions (solving several open issues)
#143
warrenmcg
closed
7 years ago
1
sleuth_results manpage does not document likelihood ratio result columns
#142
cbrueffer
closed
7 years ago
2
Add missing space in error message
#141
rakarnik
closed
7 years ago
1
Transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test
#140
apcamargo
closed
7 years ago
21
Reporting RAM requirements per sample when using multiple cores
#139
teshomem
opened
7 years ago
14
Error on reference when we use ghr38 version 90
#138
bioinfo-dirty-jobs
closed
7 years ago
2
Error in order(indices)
#137
philge
closed
7 years ago
6
Error: unexpected end of input
#136
mictadlo
closed
7 years ago
3
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