43
votes
15
replies
86k
views
9 follow
238
votes
176
replies
85k
views
73 follow
101
votes
31
replies
84k
views
18 follow
79
votes
22
replies
83k
views
16 follow
55
votes
11
replies
82k
views
8 follow
106
votes
45
replies
81k
views
30 follow
updated 9 months ago by
aswinssoman
▴
30
•
written 10.9 years ago by
Mchimich
▴
320
70
votes
20
replies
81k
views
15 follow
185
votes
43
replies
79k
views
29 follow
120
votes
8
replies
78k
views
136
votes
25
replies
77k
views
14 follow
33
votes
4
replies
77k
views
7 follow
updated 4.0 years ago by
abhijit.synl
▴
60
•
written 11.4 years ago by
Tryingtogetthere
▴
180
95
votes
27
replies
77k
views
21 follow
126
votes
24
replies
76k
views
18 follow
updated 4.1 years ago by
LuckyLuck
•
0
•
written 10.0 years ago by
deepthithomaskannan
▴
360
160
votes
62
replies
76k
views
37 follow
99
votes
16
replies
75k
views
15 follow
8.5 years ago by
Obi Griffith
20k
17
votes
12
replies
75k
views
8 follow
updated 9 months ago by
Luke
•
0
•
written 8.6 years ago by
arronslacey
▴
320
82
votes
21
replies
74k
views
13 follow
updated 3 months ago by
cmdcolin
★
3.0k
•
written 4.8 years ago by
otwtgin2010
▴
540
103
votes
12
replies
73k
views
7 follow
updated 7 months ago by
Ram
39k
•
written 11.6 years ago by
Bioscientist
★
1.7k
20
votes
2
replies
72k
views
updated 7.1 years ago by
Devon Ryan
103k
•
written 7.1 years ago by
hakimelakhrass
▴
80
122
votes
17
replies
71k
views
8 follow
43
votes
25
replies
70k
views
10 follow
updated 12.2 years ago by
Eric Fournier
★
1.4k
•
written 12.2 years ago by
Bioinfo
▴
50
22
votes
2
replies
70k
views
67
votes
18
replies
70k
views
17 follow
235
votes
45
replies
69k
views
34 follow
33
votes
17
replies
69k
views
14 follow
59
votes
15
replies
69k
views
9 follow
42
votes
14
replies
69k
views
9 follow
196
votes
44
replies
69k
views
33 follow
updated 4 months ago by
Ram
39k
•
written 10.7 years ago by
Obi Griffith
20k
188
votes
50
replies
68k
views
41 follow
updated 8 months ago by
Ram
39k
•
written 12.6 years ago by
Zhangleisdau
▴
340
138
votes
21
replies
68k
views
18 follow
54
votes
10
replies
68k
views
6 follow
updated 2.7 years ago by
naloy
•
0
•
written 4.6 years ago by
Sebastian Hesse
▴
320
24
votes
23
replies
67k
views
7 follow
updated 17 months ago by
Ram
39k
•
written 9.9 years ago by
Assa Yeroslaviz
★
1.8k
1
vote
2
replies
67k
views
updated 2.2 years ago by
Istvan Albert
98k
•
written 3.1 years ago by
geethus2009
•
0
51
votes
18
replies
66k
views
10 follow
19
votes
8
replies
66k
views
6 follow
40
votes
15
replies
66k
views
14 follow
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
updated 7 months ago by
Ram
39k
•
written 9.5 years ago by
Nicholas Spies
★
1.2k
114
votes
25
replies
65k
views
14 follow
updated 3 months ago by
Miguel
▴
10
•
written 12.3 years ago by
Pierre Lindenbaum
154k
45
votes
14
replies
65k
views
10 follow
Tutorial:
Using R in Conda
updated 11 weeks ago by
Ram
39k
•
written 2.9 years ago by
rohitsatyam102
▴
690
35
votes
9
replies
65k
views
8 follow
20
votes
15
replies
64k
views
12 follow
updated 9.7 years ago by
viv_bio
▴
50
•
written 12.6 years ago by
Studentguy
▴
70
51
votes
15
replies
64k
views
15 follow
updated 13 months ago by
Ram
39k
•
written 12.0 years ago by
Michael Petronio
▴
70
50
votes
15
replies
63k
views
12 follow
updated 3 months ago by
Ram
39k
•
written 11.9 years ago by
Bioscientist
★
1.7k
53
votes
4
replies
63k
views
40
votes
7
replies
63k
views
26
votes
10
replies
63k
views
9 follow
updated 11 weeks ago by
Ram
39k
•
written 2.2 years ago by
Nitin Narwade
★
1.3k
25
votes
5
replies
61k
views
7 follow
updated 10.6 years ago by
JC
13k
•
written 10.6 years ago by
siddharth.sethi5
▴
270
8
votes
6
replies
61k
views
updated 9.4 years ago by
r.follador
▴
90
•
written 9.4 years ago by
HG
★
1.2k
361
votes
57
replies
61k
views
43 follow
updated 8 months ago by
Kevin Blighe
85k
•
written 13.2 years ago by
Istvan Albert
98k
11
votes
9
replies
60k
views
7 follow
updated 6 months ago by
Devarakonda
•
0
•
written 8.4 years ago by
vigneshprbh37
▴
30
Recent Locations •
All
United States, just now
United States, 1 minute ago
Bologna, 1 minute ago
London, 2 minutes ago
United States, 3 minutes ago
United States, 5 minutes ago
United States, 7 minutes ago
Recent Awards •
All
Popular Question to
tarek.mohamed
▴
350
Popular Question to
carlopecoraro2
★
2.3k
Popular Question to
kamanovae
▴
80
Popular Question to
Lila M
★
1.2k
Popular Question to
oakhamwolf
▴
20
Commentator to
Istvan Albert
98k
Recent Replies
Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴
40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★
2.8k
ok interesting.
Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴
40
Bedtools window piped into genomecov?
https://bedtools.readthedocs.io/en/latest/content/tools/window.html
https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
•
0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
•
0
```r
query <- GDCquery(
project = "TCGA-THCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
•
0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files
Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index
by
ashleymb1116
•
0
Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
Traffic: 2618 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6