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116,769 results • Page
1 of 2336
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
35
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
24 minutes ago by
brandon
• 0
0
votes
1
reply
48
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
2 hours ago by
mropri
▴ 150
0
votes
0
replies
41
views
Gene ontology and homologs
geneontology
bioinformatics
gene
updated 50 minutes ago by
GenoMax
142k • written 3 hours ago by
beshka194
• 0
0
votes
0
replies
123
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 hours ago by
arctic
▴ 40 • written 2 days ago by
M.
▴ 30
0
votes
0
replies
37
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
5 hours ago by
KHURRAM SHAHZAD
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
1
vote
2
replies
128
views
install package
package
install
updated 4 hours ago by
Pine
▴ 10 • written 8 hours ago by
snajafy
• 0
0
votes
0
replies
47
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
6 hours ago by
Christopher
• 0
2
votes
1
reply
139
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
filtering
independent
linkage
8 hours ago by
Jautis
▴ 540
1
vote
2
replies
211
views
Association study using SNP data
Association
Allele
Parentage
SNP
8 hours ago by
drajangirija
• 0
0
votes
0
replies
48
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
10 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
59
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
10 hours ago by
DGTool
• 0
0
votes
0
replies
57
views
Seurat V5 integration
Seurat
samples
integration
combine
12 hours ago by
starswillfade
▴ 10
0
votes
0
replies
67
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
16 hours ago by
Yoosef
▴ 60
0
votes
1
reply
233
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 9 hours ago by
GenoMax
142k • written 18 hours ago by
tulip
• 0
2
votes
3
replies
296
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 21 hours ago by
Gordon Smyth
★ 7.1k • written 2 days ago by
SHN
▴ 40
4
votes
2
replies
186
views
GRCh38.gmap file
gnomix
gmap
1 day ago by
lorena9132
▴ 10
2
votes
3
replies
756
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 1 day ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
2
replies
193
views
creating batch colum for batch correction
batch-correction
combat
updated 1 day ago by
Ram
43k • written 1 day ago by
Expert
▴ 10
1
vote
4
replies
273
views
Segmentation error while using a tool
smalt
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Ruqaiya
• 0
0
votes
1
reply
106
views
Help with DGEList function
DGEList
R
updated 1 hour ago by
marco.barr
▴ 90 • written 1 day ago by
Natali
• 0
0
votes
0
replies
90
views
Homer motif analysis
Homer
1 day ago by
daffodil
▴ 10
0
votes
1
reply
134
views
HCL database download
database
HCL
human
updated 1 day ago by
GenoMax
142k • written 1 day ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
15 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
242
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 1 day ago by
chrchang523
10k • written 5 days ago by
8armed
• 0
0
votes
5
replies
293
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 1 day ago by
chrchang523
10k • written 2 days ago by
curious
▴ 750
0
votes
0
replies
117
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 1 day ago by
Ram
43k • written 2 days ago by
deepak180001
• 0
0
votes
1
reply
164
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 1 day ago by
Ram
43k • written 2 days ago by
Rob
▴ 170
0
votes
1
reply
158
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Ximena
• 0
0
votes
1
reply
155
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 1 day ago by
Ram
43k • written 2 days ago by
Valentina
• 0
0
votes
6
replies
356
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
Erina
• 0
0
votes
1
reply
153
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
kalavattam
▴ 190
1
vote
3
replies
208
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
5 hours ago by
Lada
▴ 30
0
votes
0
replies
114
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
2 days ago by
Emilie
• 0
0
votes
0
replies
112
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
2 days ago by
Javier
• 0
0
votes
1
reply
202
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 1 day ago by
Thanujay S
• 0 • written 2 days ago by
yahn
• 0
0
votes
0
replies
108
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
2 days ago by
mikemakaveli1
• 0
2
votes
2
replies
187
views
Raw counts using stringtie
stringtie
RNA-seq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
107
views
Modify plot R mtDNA indel
plot
mtDNA
R
2 days ago by
marco.barr
▴ 90
0
votes
0
replies
216
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
2 days ago by
NorbertK
• 0
2
votes
2
replies
194
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 1 day ago by
Ram
43k • written 2 days ago by
carolofharvest
▴ 30
9
votes
9
replies
537
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by
Ram
43k • written 6 days ago by
carolofharvest
▴ 30
0
votes
2
replies
212
views
Downloading older version of a tool
Alignment
tools
1 day ago by
Ruqaiya
• 0
0
votes
0
replies
125
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
2 days ago by
rustykb
▴ 20
1
vote
1
reply
157
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 1 day ago by
Ram
43k • written 2 days ago by
adi.gershon1
• 0
3
votes
5
replies
246
views
Generating mpileup file using samtools
mpileup
samtools
updated 2 days ago by
Joe
21k • written 2 days ago by
Ruqaiya
• 0
0
votes
5
replies
321
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 2 days ago by
b.contreras.moreira
▴ 180 • written 3 days ago by
JH
• 0
1
vote
3
replies
266
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Qi
• 0
0
votes
0
replies
122
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
2 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
267
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 2 days ago by
dthorbur
★ 1.9k • written 2 days ago by
Vijith
▴ 30
116,769 results • Page
1 of 2336
Recent Votes
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
A: Fold change - a final explanation
Answer: sc/snRNASeq using cell ranger parameters
mitochondria in single nuclear RNAseq
Answer: Association study using SNP data
Comment: agilent human all exon sureselct v7 bed file
Recent Locations •
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Pierre Lindenbaum
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qudrat.nii
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Recent Replies
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
by
brandon
• 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
by
Pierre Lindenbaum
161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
Comment: Help with DGEList function
by
marco.barr
▴ 90
Are you sure you've loaded the library properly? Have you checked if edgeR is ticked in the list of installed packages? Double-check it. If…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi, I just wanted to update that IEGscore and PCNAscore were linearly dependent (or linear combinations of each other). I tested this using…
Comment: TaxID mapping file
by
Lada
▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package
by
Pine
▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file
by
MiladAD
▴ 10
God bless you man.
Answer: install package
by
Mathew
▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
Lada
▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
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