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50 results • Page
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Showing top results for tag:
KEGG
•
reset
0
votes
0
replies
70
views
Confusing Pathway Analysis Results from DAVID
DAVID
Reactome
KEGG
1 day ago by
saamhasan55
▴ 10
5
votes
3
replies
440
views
blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) databases
KEGG
KOG
blast
GO
updated 28 days ago by
Mensur Dlakic
★ 28k • written 29 days ago by
analyst
▴ 50
1
vote
2
replies
1.4k
views
pathview - cannot open URL : HTTP status was '403 Forbidden'
R
kegg
pathview
updated 5 weeks ago by
lianchee11
▴ 50 • written 2.2 years ago by
Itamar
▴ 10
0
votes
0
replies
201
views
Workflow for functional analysis of differential gene core modules: KEGG, GSEA, and GO enrichment
gsea
ppi-network
enrichment-analysis
kegg
8 weeks ago by
mizzika
• 0
0
votes
1
reply
799
views
Enrichment analysis guide for msu7 rice genome
transcriptome
KEGG
MSU7
rice
GOenrichment
updated 9 weeks ago by
白
• 0 • written 13 months ago by
sumitra.20
• 0
0
votes
5
replies
479
views
Pathway analysis for DGEList
KEGG
Pathway_analysis
GO
gene_expression
DGEList
updated 11 weeks ago by
BioinfGuru
★ 2.1k • written 12 weeks ago by
bioinfo1994
• 0
0
votes
0
replies
178
views
KEGG pathways analysis (ko and map IDs)
ko
kegg
pathway
map
updated 3 months ago by
GenoMax
145k • written 3 months ago by
manekineko
▴ 10
0
votes
0
replies
261
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
4 months ago by
doramora
▴ 10
0
votes
0
replies
197
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 4 months ago by
Ram
44k • written 4 months ago by
letizia.ottaviani
• 0
0
votes
0
replies
186
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
4 months ago by
dlera.lozano
▴ 10
0
votes
0
replies
238
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
4 months ago by
O.rka
▴ 740
1
vote
1
reply
319
views
API kegg - IndexError: list index out of range
kegg
API
updated 4 months ago by
Nyksubuz
▴ 20 • written 4 months ago by
mirwa.zidi93
• 0
2
votes
7
replies
1.2k
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 4 months ago by
letizia.ottaviani
• 0 • written 5 months ago by
sansan96
▴ 130
2
votes
2
replies
640
views
GSEA on non-model organisms: How to handle duplicated KEGG KO
KEGG
GSEA
clusterProfiler
GhostKOALA
updated 5 months ago by
alserg
▴ 940 • written 5 months ago by
mksaad28
• 0
0
votes
0
replies
188
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
6 months ago by
Chris
▴ 340
0
votes
0
replies
215
views
MG-RAST KEGG KO Search
mg-rast
kegg
metagenomics
ko
6 months ago by
Jeremy
▴ 920
0
votes
5
replies
648
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
6 months ago by
Maxwell
▴ 20
0
votes
0
replies
191
views
Help plotting enrichment results - kegg terms
Enrichment-analysis
KEGG
updated 6 months ago by
Ram
44k • written 6 months ago by
DByter
• 0
0
votes
0
replies
299
views
Enzyme in Pathview
r
metabolomic
kegg
pathview
updated 7 months ago by
Pierre Lindenbaum
164k • written 7 months ago by
CECEL
• 0
2
votes
6
replies
895
views
GO and KEGG
GO
bulk-RNA-seq
Rstudio
KEGG
updated 7 months ago by
jv
★ 1.8k • written 7 months ago by
matteo.levorato
• 0
0
votes
0
replies
259
views
KEGG orthology ID to E. coli gene symbol
symbol
KEGG
convert
8 months ago by
sooni
▴ 20
0
votes
0
replies
288
views
Pathview modifies LFC genes. Is this normal?
gage
pathview
KEGG
R
8 months ago by
Alex
• 0
0
votes
0
replies
271
views
Gold Standard Gene Regulatory Network Data for Human Cell Cycle
pathway
kegg
updated 8 months ago by
Ram
44k • written 8 months ago by
Melinda
• 0
1
vote
10
replies
1.2k
views
How to obtain the gene set of KEGG module
R
gene-set
KEGG
8 months ago by
xingyu
▴ 10
0
votes
1
reply
550
views
Enrichment dotplot color
KEGG
R
GO
Enrichment
dotplot
updated 9 months ago by
rpolicastro
13k • written 9 months ago by
Grace
• 0
1
vote
3
replies
691
views
GO, KEGG, GSEA analysis with ~5 DEGs
GO
KEGG
updated 9 months ago by
Istvan Albert
101k • written 9 months ago by
foejvs546
▴ 20
0
votes
0
replies
334
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
10 months ago by
Assa Yeroslaviz
★ 1.9k
4
votes
2
replies
590
views
KEGG DATABASE
DATABASE
KEGG
updated 9 months ago by
jv
★ 1.8k • written 10 months ago by
Sijjil
• 0
0
votes
0
replies
396
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
10 months ago by
bioinfo
▴ 150
0
votes
0
replies
294
views
KEGG module and abundance of its KEGG Orthologs for functioning
function
kegg
abundance
10 months ago by
Jonathan Yoou
▴ 60
0
votes
0
replies
315
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview
KEGG
10 months ago by
B.N.
▴ 10
0
votes
0
replies
478
views
Trouble Adding Log Fold Changes to KEGG Pathway Visualization
KEGG
RStudio
updated 10 months ago by
Ram
44k • written 10 months ago by
ramirj49
• 0
4
votes
4
replies
1.0k
views
Combining GO and KEGG enrichments
Cytoscape
KEGG
network
RNASeq
GO
10 months ago by
David R
▴ 20
0
votes
5
replies
1.0k
views
R Kegg Need help ASAP
KEGG
RStudio
updated 11 months ago by
Ram
44k • written 11 months ago by
ramirj49
• 0
0
votes
0
replies
373
views
RAP.ID to KEGG ID converter
RAP.ID
KEGG
RStudio
updated 11 months ago by
Ram
44k • written 11 months ago by
ramirj49
• 0
0
votes
2
replies
751
views
To draw a heatmap displaying DEGs associated with a specific KEGG pathway.
heatmap
KEGG
DEG
updated 11 months ago by
yhdist
▴ 70 • written 11 months ago by
Biostars2200
• 0
0
votes
0
replies
291
views
KEGG ribosomal gene found in metatranscriptome despite removing rRNA sequences
rRNA
KEGG
metatranscriptomics
11 months ago by
kmat
• 0
1
vote
2
replies
974
views
KEGG Pathway analysis for non-model organism using goseq
non-model-organism
KEGG
DEG
11 months ago by
analyst
▴ 50
0
votes
0
replies
395
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR
LogFC
pathview
KEGG
12 months ago by
Ann
▴ 40
5
votes
3
replies
1.5k
views
interpreting results from pathway analysis
RNA-seq
kegg
clusterprofiler
GSEA
pathway-analysis
updated 12 months ago by
Ram
44k • written 14 months ago by
kng
▴ 40
0
votes
1
reply
690
views
Gene set enrichment analysis / Kegg analysis
kegg
DGE
RNAseq
GSEA
DESeq2
updated 13 months ago by
Manuel Sokolov Ravasqueira
▴ 110 • written 13 months ago by
fakeeha
• 0
0
votes
4
replies
777
views
KEGG adnotation
vizualization
hordeum
biologicalprocess
KEGG
updated 13 months ago by
Eshwari
▴ 10 • written 13 months ago by
martta95
▴ 10
7
votes
6
replies
4.0k
views
7 follow
KEGG pathway maps
KEGG
RNA-Seq
updated 14 months ago by
liux.bio
▴ 360 • written 7.9 years ago by
dazhudou1122
▴ 140
2
votes
2
replies
3.3k
views
From Kegg - Kaas to MetaCyc
kegg
metacyc
rna-seq
updated 14 months ago by
ron.caspi
▴ 10 • written 10.5 years ago by
charly.blanche.t
▴ 20
0
votes
0
replies
295
views
Extract KEGG pathway hierarchy
kegg
hierarchy
api
updated 14 months ago by
Ram
44k • written 14 months ago by
kamalika
• 0
0
votes
0
replies
418
views
What criteria are used to determine significant HMMER hits?
kegg
protein
kofamscan
annotation
metagenomics
14 months ago by
O.rka
▴ 740
1
vote
2
replies
623
views
Downstream analysis of DEG for non-model organisms.
Axolotl
KEGG
GO
GSEA
14 months ago by
georgii.vdovin
• 0
0
votes
1
reply
964
views
Which KEGG Database to use for DIAMOND annotation of predicted gene coding regions?
metatranscriptomics
KEGG
RNA-seq
prodigal
DIAMOND
updated 14 months ago by
Asaf
10k • written 14 months ago by
Lily
• 0
1
vote
0
replies
429
views
Looking to expand annotation of kegg in data frame R
kegg
orthologs
annotations
R
updated 14 months ago by
zx8754
12k • written 14 months ago by
microecologist93
▴ 20
0
votes
0
replies
388
views
Visualise three samples with KO abundance using Pathview
KEGG
pathview
R
KO
15 months ago by
AliceLee
• 0
50 results • Page
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Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
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145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
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Please do not ask questions unrelated to the original post in this thread. Post a new question.
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I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
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One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
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• 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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• 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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• 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and: ``` rsem-calculate-expression …
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oops ``` file *.out.bam KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field KO1_2Aligned.toTranscriptome.out.bam: …
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read https://github.com/samtools/samtools/blob/develop/sam_view.c * allocate a new bam1_t* b = bam_init1 * open the input file: sam_op…
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Thank you, it worked almost after two months of struggle, I nearly deleted everything and reinstalled it, I assume the problem was someth…
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