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32 results • Page
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0
votes
8
replies
385
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What does it mean single base resolution in sequencing?
SNP
sequencing
updated 15 hours ago by
LauferVA
4.2k • written 2 days ago by
jinyu
▴ 10
1
vote
8
replies
420
views
Downsampling fastq file
downsample
fastq
18 hours ago by
marco.barr
▴ 80
5
votes
6
replies
396
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 18 hours ago by
me
▴ 760 • written 1 day ago by
Mariana
▴ 40
2
votes
4
replies
266
views
from row count to tpm
tpm
row-count
normalization
updated 19 hours ago by
Ram
43k • written 8 days ago by
michelafrancesconi9
▴ 20
0
votes
4
replies
199
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 22 hours ago by
Michael
54k • written 23 hours ago by
Riccardo
▴ 10
0
votes
3
replies
232
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
kim
• 0
0
votes
3
replies
365
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
20 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
204
views
KEGG Pathways
r
RNA-seq
updated 17 hours ago by
Ram
43k • written 1 day ago by
Sudip
• 0
0
votes
3
replies
178
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 14 hours ago by
GenoMax
141k • written 19 hours ago by
jeffrey.maurer.informatics
• 0
0
votes
3
replies
228
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 hours ago by
LChart
3.9k • written 1 day ago by
kl
▴ 10
0
votes
3
replies
173
views
Telescope issue
Telescope
RNA-seq
updated 8 hours ago by
GenoMax
141k • written 16 hours ago by
eleven11
• 0
0
votes
2
replies
172
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
19 hours ago by
matteo.levorato
• 0
3
votes
2
replies
321
views
Extract protein sequence
fasta
alignment
blast
16 hours ago by
anna
▴ 20
1
vote
2
replies
169
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 19 hours ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
2
replies
156
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
Dora
▴ 10
2
votes
2
replies
143
views
p-value in CIBERSORT
CIBERSORT
p-value
2 hours ago by
michelafrancesconi9
▴ 20
0
votes
1
reply
109
views
unable to get feature count results
featureCounts
updated 19 hours ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
1
reply
92
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 6 hours ago by
Ram
43k • written 9 hours ago by
rianna.collins
• 0
1
vote
1
reply
156
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
14 hours ago by
heelpPlease
• 0
0
votes
1
reply
143
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 14 hours ago by
Ram
43k • written 19 hours ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
144
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
updated 14 hours ago by
Ram
43k • written 19 hours ago by
Nafi
• 0
0
votes
1
reply
64
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 50 minutes ago by
i.sudbery
19k • written 11 hours ago by
Edmond
• 0
0
votes
1
reply
177
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 6 hours ago by
Ram
43k • written 12 hours ago by
Dr Huma Naz
• 0
0
votes
0
replies
101
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 20 hours ago by
Ram
43k • written 21 hours ago by
Chakri
• 0
0
votes
0
replies
78
views
barcode of TCR-sequencing
barcode
22 hours ago by
yueli7
▴ 250
0
votes
0
replies
60
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
12 hours ago by
O.rka
▴ 710
0
votes
0
replies
80
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 19 hours ago by
Ram
43k • written 21 hours ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
82
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 22 hours ago by
Ram
43k • written 23 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
55
views
DESeq2 processing problems
deseq2
R
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
jagdish7921
• 0
0
votes
0
replies
81
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
19 hours ago by
sarphilsar
• 0
0
votes
0
replies
75
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 14 hours ago by
Ram
43k • written 17 hours ago by
J
• 0
0
votes
0
replies
78
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 21 hours ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
32 results • Page
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Answer: Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC
Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
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Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
Comment: Programmatically retrieving positions of protein active site residues
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Recent Replies
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
by
i.sudbery
19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue
by
GenoMax
141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
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