NUStatBioinfo DegNorm issues

NUStatBioinfo / DegNorm

Normalizing RNA degradation in RNA-seq data

https://nustatbioinfo.github.io/DegNorm/

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issues

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processing multiple datasets

#50 marce-sarrias opened 9 months ago
0
Bump scipy from 0.19.1 to 1.10.0 in /config

#49 dependabot[bot] opened 1 year ago
0
some help running degNorm

#48 dllahr closed 1 year ago
2
Bump joblib from 0.12.2 to 1.2.0 in /config

#47 dependabot[bot] opened 1 year ago
0
Bump numpy from 1.13.3 to 1.22.0 in /config

#46 dependabot[bot] opened 2 years ago
0
Memory issues with mpi4py and pickle

#45 alyxgray7 opened 2 years ago
2
DegNorm CLI runs dying

#44 lquayle88 closed 2 years ago
1
Problem running DegNorm R package

#43 paawanpoudel opened 3 years ago
0
attempt to fix indexing error, #34

#42 ffineis closed 4 years ago
0
Error re-running a failed run

#41 iS4i4S opened 4 years ago
2
Allow user to identify gene names by `gene_id` or `gene_name`

#40 ffineis opened 4 years ago
0
Job is killed during the initial NMF-OA iteration

#39 cheffelfinger closed 4 years ago
2
Feature/gtf protects etc

#38 ffineis closed 4 years ago
0
degnorm_mpi exits with code 9

#37 senlidk closed 4 years ago
0
IndexError: list index out of range (DegNorm)

#36 miyakokodama closed 4 years ago
3
TypeError: unsupported operand type(s) for -: 'str' and 'int' (DegNorm)

#35 KosarHooshmand closed 4 years ago
5
Error at 'begin coverage matrix processing'

#34 MadeleineCarruthers closed 4 years ago
2
Error when loading reads

#33 symbiologist opened 4 years ago
6
Hotfix/issues

#32 ffineis closed 4 years ago
0
'dict' object has no attribute 'as_dict'

#31 artagmaz closed 4 years ago
10
Is there anyway of continuing without restarting?

#30 mhagemann86 closed 4 years ago
3
Hotfix/read gene join

#29 ffineis closed 5 years ago
0
ValueError: Usecols do not match names. & ValueError: file {0} must have the 9 mandatory .gtf columns

#28 mhagemann86 closed 5 years ago
1
KeyError: 'None of [read_id\n53 52280\n54 52282\n55 52282\n56 52282\n57 52286\n60 52342\n68 52668\n69 52668\n76 52721\n77 52721\n78 52722\n79 52722\n80 52722\n81 52725\n82 52730\n83 52730\n84 52730\n85 52731\n86 52732\n87 52737\n88 52737\n89 52745\n90 52751\n91 52754\n92 52756\n93 52756\n94 52758\n95 52758\n96 52758\n97 52758\n ... \n192 58748\n193 58749\n194 58749\n195 58750\n196 58750\n197 58756\n198 58756\n199 58760\n200 58762\n201 58767\n202 58769\n203 58770\n204 58778\n205 58786\n206 58786\n207 58794\n208 58795\n209 58795\n210 58811\n211 58811\n212 58811\n213 58812\n214 58812\n215 58812\n216 58813\n217 58813\n218 58816\n219 58857\n220 59111\n221 59238\nName: pos, Length: 140, dtype: int64] are in the [index]'

#27 sommikim closed 5 years ago
1
attempt to fix #25

#26 ffineis closed 5 years ago
0
File "/newlustre/home/clad/miniconda3/envs/degnorm/lib/python3.6/site-packages/pandas/core/indexing.py", line 1418, in _has_valid_type (key, self.obj._get_axis_name(axis))) KeyError: 'None of [read_id\ .........Name: pos, dtype: int64] are in the [index]'

#25 Yali1989 closed 5 years ago
11
Feature/etc updates

#24 ffineis closed 5 years ago
0
CPU usage

#23 josruirod closed 5 years ago
5
hotfix for hard clipping aligned reads

#22 ffineis closed 5 years ago
0
Recurring error: UnboundLocalError: local variable 'augment' referenced before assignment

#21 BMBlobner closed 5 years ago
4
contact page

#20 ffineis closed 5 years ago
0
Feature/accounting (+ GB publishing release)

#19 ffineis closed 5 years ago
0
Feature/accounting (+ publish release)

#18 ffineis closed 5 years ago
0
Feature/gtf speedup

#17 ffineis closed 5 years ago
0
fix git clone url, add samtools cmds to example usage docs

#16 ffineis closed 5 years ago
0
Feature/mpi new

#15 ffineis closed 5 years ago
1
Feature/bam files

#14 ffineis closed 5 years ago
1
touch up output docs

#13 ffineis closed 5 years ago
0
Feature/docs

#12 ffineis closed 5 years ago
0
Feature/get coverage

#11 ffineis closed 5 years ago
0
Feature/singlereads

#10 ffineis closed 5 years ago
0
add travis ci badge to readme

#9 ffineis closed 5 years ago
0
very first attempt at travis file

#8 ffineis closed 5 years ago
0
Feature/binmatch

#7 ffineis closed 5 years ago
0
update visualization code

#6 ffineis closed 5 years ago
0
Feature/binmatch

#5 ffineis closed 5 years ago
0
Feature/random debugs

#4 ffineis closed 5 years ago
0
Feature/random debugs

#3 ffineis closed 5 years ago
0
Feature/warm start

#2 ffineis closed 5 years ago
0
Feature/pandoc

#1 ffineis closed 5 years ago
0