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44 results • Page
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0
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52
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 1 hour ago by
Ram
43k • written 4 hours ago by
rianna.collins
• 0
0
votes
0
replies
34
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
6 hours ago by
Edmond
• 0
0
votes
0
replies
40
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
6 hours ago by
O.rka
▴ 710
0
votes
1
reply
80
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 1 hour ago by
Ram
43k • written 6 hours ago by
Dr Huma Naz
• 0
2
votes
1
reply
108
views
p-value in CIBERSORT
CIBERSORT
p-value
updated 8 hours ago by
Ram
43k • written 14 hours ago by
michelafrancesconi9
▴ 20
0
votes
3
replies
137
views
Telescope issue
Telescope
RNA-seq
updated 2 hours ago by
GenoMax
141k • written 11 hours ago by
eleven11
• 0
0
votes
0
replies
60
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 8 hours ago by
Ram
43k • written 11 hours ago by
J
• 0
5
votes
6
replies
363
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 13 hours ago by
me
▴ 760 • written 1 day ago by
Mariana
▴ 40
0
votes
0
replies
64
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
13 hours ago by
sarphilsar
• 0
0
votes
1
reply
125
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 8 hours ago by
Ram
43k • written 13 hours ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
128
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
updated 8 hours ago by
Ram
43k • written 13 hours ago by
Nafi
• 0
0
votes
3
replies
154
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 8 hours ago by
GenoMax
141k • written 13 hours ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
147
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 14 hours ago by
GenoMax
141k • written 20 hours ago by
Dora
▴ 10
0
votes
0
replies
86
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 15 hours ago by
Ram
43k • written 15 hours ago by
Chakri
• 0
0
votes
0
replies
73
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 14 hours ago by
Ram
43k • written 16 hours ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
188
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 16 hours ago by
Michael
54k • written 18 hours ago by
Riccardo
▴ 10
0
votes
0
replies
68
views
barcode of TCR-sequencing
barcode
16 hours ago by
yueli7
▴ 250
0
votes
0
replies
73
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 17 hours ago by
Ram
43k • written 18 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
70
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 16 hours ago by
Ram
43k • written 18 hours ago by
Alexandros
• 0
0
votes
1
reply
100
views
unable to get feature count results
featureCounts
updated 14 hours ago by
Ram
43k • written 18 hours ago by
Ravita
• 0
0
votes
0
replies
69
views
Subsetting and merging back Seurat Object brings different results
Seurat
18 hours ago by
Bine
▴ 60
0
votes
3
replies
187
views
KEGG Pathways
r
RNA-seq
updated 12 hours ago by
Ram
43k • written 19 hours ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 19 hours ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
73
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
19 hours ago by
Bine
▴ 60
0
votes
1
reply
221
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
20 hours ago by
David Langenberger
11k
0
votes
0
replies
73
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
20 hours ago by
8armed
• 0
0
votes
1
reply
122
views
Deseq2
Deseq2
updated 21 hours ago by
Jack Tierney
▴ 360 • written 22 hours ago by
Sudip
• 0
1
vote
1
reply
154
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 21 hours ago by
Michael
54k • written 1 day ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
195
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 21 hours ago by
Lluís R.
★ 1.2k • written 23 hours ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
127
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 22 hours ago by
ATpoint
82k • written 22 hours ago by
Sudip
• 0
1
vote
2
replies
160
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 14 hours ago by
Ram
43k • written 22 hours ago by
Ravita
• 0
0
votes
0
replies
66
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
22 hours ago by
Adyasha
• 0
0
votes
3
replies
213
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 8 hours ago by
LChart
3.9k • written 1 day ago by
kl
▴ 10
0
votes
3
replies
221
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 18 hours ago by
GenoMax
141k • written 1 day ago by
kim
• 0
3
votes
2
replies
309
views
Extract protein sequence
fasta
alignment
blast
10 hours ago by
anna
▴ 20
0
votes
4
replies
204
views
Genbank File Format
gbkformat
21 hours ago by
alenew.am
• 0
0
votes
2
replies
170
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
13 hours ago by
matteo.levorato
• 0
37
votes
24
replies
1.7k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 20 hours ago by
i.sudbery
19k • written 3 days ago by
noodle
▴ 580
0
votes
8
replies
375
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 10 hours ago by
LauferVA
4.2k • written 2 days ago by
jinyu
▴ 10
0
votes
3
replies
363
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
14 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
156
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
8 hours ago by
heelpPlease
• 0
2
votes
4
replies
265
views
from row count to tpm
tpm
row-count
normalization
updated 14 hours ago by
Ram
43k • written 8 days ago by
michelafrancesconi9
▴ 20
1
vote
8
replies
415
views
Downsampling fastq file
downsample
fastq
12 hours ago by
marco.barr
▴ 80
0
votes
10
replies
466
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 20 hours ago by
i.sudbery
19k • written 8 days ago by
Patadu94
• 0
44 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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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, …
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
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