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116,574 results • Page
1 of 2332
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0
votes
0
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5
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Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
hetero
Seurat
modelHomotypic
DoubletFinder
8 minutes ago by
Jeyong
• 0
0
votes
0
replies
12
views
To get p-values for the TPM
P-value
TPM
RSEM
30 minutes ago by
VITALA
• 0
0
votes
0
replies
20
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
1 hour ago by
Aaliya
• 0
0
votes
1
reply
63
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
updated 2 hours ago by
yxwucq
• 0 • written 7 hours ago by
mropri
▴ 150
1
vote
2
replies
80
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 1 hour ago by
analyst
▴ 20 • written 6 hours ago by
lorena9132
• 0
0
votes
0
replies
43
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
7 hours ago by
Kash
▴ 110
795
votes
167
replies
141k
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
5
votes
2
replies
175
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 7 hours ago by
geneontologyhelp
▴ 380 • written 1 day ago by
catherine.teyssier
• 0
0
votes
1
reply
129
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 7 hours ago by
Istvan Albert
100k • written 1 day ago by
Abeer
• 0
0
votes
4
replies
205
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 7 hours ago by
swbarnes2
14k • written 1 day ago by
dxj294
• 0
0
votes
1
reply
65
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 8 hours ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
87
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 7 hours ago by
GenoMax
141k • written 9 hours ago by
v.berriosfarias
▴ 140
0
votes
1
reply
124
views
Seurat merge and batch correction
Seurat
updated 9 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
1
vote
1
reply
92
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 9 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
Biostar
2.7k
1
vote
1
reply
84
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 10 hours ago by
GenoMax
141k • written 10 hours ago by
heelpPlease
• 0
2
votes
9
replies
737
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 5 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
296
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
3 hours ago by
atowns21
• 0
0
votes
1
reply
88
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 10 hours ago by
bk11
★ 2.3k • written 11 hours ago by
alphaflylizard
• 0
3
votes
3
replies
146
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 11 hours ago by
GenoMax
141k • written 12 hours ago by
Estevão
• 0
0
votes
3
replies
172
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 8 hours ago by
Istvan Albert
100k • written 13 hours ago by
Dylan
• 0
0
votes
1
reply
75
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 12 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
Lada
▴ 30
4
votes
11
replies
416
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 5 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
3
votes
7
replies
415
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 11 hours ago by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
0
votes
0
replies
54
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
14 hours ago by
ohtang7
▴ 40
2
votes
0
replies
72
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 15 hours ago by
Ram
43k • written 15 hours ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
371
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 16 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
100
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 17 hours ago by
GenoMax
141k • written 17 hours ago by
Srinka
▴ 20
8
votes
5
replies
4.7k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
4
replies
188
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 15 hours ago by
GenoMax
141k • written 17 hours ago by
njornet
▴ 20
5
votes
4
replies
551
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
54 minutes ago by
kirillkirilenko
▴ 40
0
votes
0
replies
60
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 15 hours ago by
Ram
43k • written 18 hours ago by
SHREYA
• 0
0
votes
3
replies
328
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 18 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
67
views
Merging replicates from Encode project
CHIP-seq
encode
18 hours ago by
Nurken
• 0
1
vote
3
replies
166
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
19 hours ago by
WouterDeCoster
47k
0
votes
3
replies
168
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 17 hours ago by
mchour
• 0 • written 20 hours ago by
rhossen
• 0
1
vote
1
reply
127
views
WGCNA preservation analysis
WGCNA
preservation
updated 20 hours ago by
Michael
54k • written 21 hours ago by
michael.flower.14
▴ 180
0
votes
3
replies
177
views
some error in building kraken2 database
metagenome
kraken2
4 hours ago by
Art1ess
• 0
0
votes
1
reply
102
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 15 hours ago by
bk11
★ 2.3k • written 20 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
105
views
Plots for DNA methylation data
plots
DNA
methylation
updated 18 hours ago by
GenoMax
141k • written 22 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
460
views
python file for coding potential calculator
cpc2.py
updated 22 hours ago by
atharvakarkare14
▴ 10 • written 5 days ago by
Ashok
• 0
1
vote
1
reply
133
views
Failed kmer content
kmer
illumina
ngs
updated 15 hours ago by
Ram
43k • written 23 hours ago by
Kasturi
• 0
0
votes
2
replies
165
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 8 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
115
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
1 day ago by
yxwucq
• 0
0
votes
0
replies
68
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 14 hours ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
6
replies
267
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
10 hours ago by
Sd
• 0
0
votes
2
replies
153
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
1 day ago by
sainavyav22
• 0
0
votes
1
reply
122
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
259
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
2
votes
7
replies
270
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 hour ago by
Istvan Albert
100k • written 1 day ago by
Κοσμάς
• 0
0
votes
0
replies
98
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
116,574 results • Page
1 of 2332
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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