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120,710 results • Page
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Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 8 hours ago by
S
• 0 • written 28 days ago by
s
• 0
0
votes
1
reply
69
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 3 hours ago by
GenoMax
149k • written 9 hours ago by
brutonk
• 0
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
42
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
10 hours ago by
Mllepnos
• 0
0
votes
0
replies
58
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
11 hours ago by
ATRX
★ 1.2k
1
vote
0
replies
46
views
Tool:
PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment
function
GO
goterms
geneontology
12 hours ago by
geneontologyhelp
▴ 450
0
votes
0
replies
62
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
14 hours ago by
Ram
45k
2
votes
1
reply
157
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
updated 15 hours ago by
grover.sandeep
▴ 20 • written 2 days ago by
s.may-wilson
▴ 50
0
votes
0
replies
64
views
News:
Multi-Omics Integration with Machine Learning — Online Course!
Machine-Learning
Multi-Omics
Depp-Learning
Data-Integration
BigData
15 hours ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
115
views
Alignment algorithm for DNA sequencing
sequencing
data
DNA
updated 16 hours ago by
ATpoint
87k • written 16 hours ago by
QX
▴ 70
0
votes
1
reply
113
views
RepeatMasker UCSC track
RepeatMasker
updated 17 hours ago by
Michael
55k • written 21 hours ago by
frarodmar17
• 0
0
votes
0
replies
76
views
rarefaction curve metagenomic reads show species saturation around 100 000 reads
metagenomics
rarefaction
kraken2
20 hours ago by
rDNA
▴ 20
0
votes
4
replies
323
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 14 hours ago by
jared.andrews07
★ 18k • written 3 days ago by
Pumla
• 0
9
votes
21
replies
7.6k
views
12 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 22 hours ago by
bagdevi.mishra
▴ 110 • written 6 months ago by
Martina
• 0
0
votes
2
replies
140
views
Looking up gene name from mRNA ID using biomaRt
R
mRNA
biomaRt
updated 15 hours ago by
Ram
45k • written 1 day ago by
Khôi
• 0
0
votes
0
replies
94
views
Interpreting negative gap length in MUMMER4
mummer
translocation
1 day ago by
cedric.blais
▴ 20
0
votes
0
replies
81
views
Uncertainty about deepTools computeMatrix options for RNA modifications
deepTools
metagene
computeMatrix
1 day ago by
Kyle
• 0
0
votes
0
replies
80
views
News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
1 day ago by
soledad.esteban
• 0
6
votes
6
replies
481
views
Multiple factors in DESeq2
deseq2
1 day ago by
noodlejackson
▴ 40
10
votes
2
replies
227
views
Why do RNAseq reads align to non-gene regions of the bacterial genome?
RNAseq
transcription
updated 1 day ago by
i.sudbery
21k • written 2 days ago by
Texx
▴ 40
1
vote
1
reply
180
views
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genomes
star
trinity
rnaseq
updated 1 day ago by
Ram
45k • written 1 day ago by
zizigolu
★ 4.3k
3
votes
7
replies
241
views
nanopore variant calling
pacBio
long-read
nanopore
updated 15 hours ago by
colindaven
7.3k • written 1 day ago by
Meghan.T
• 0
0
votes
3
replies
221
views
enrichGo problem
enrichGo
updated 15 hours ago by
Arup Ghosh
3.3k • written 1 day ago by
mimijane1664
• 0
1
vote
4
replies
222
views
Seeking Help for Reanalysis of Raw WES Data
WES
updated 1 day ago by
Jeremy Leipzig
23k • written 1 day ago by
lidia.manczak
• 0
1
vote
8
replies
215
views
Biscuit Alignment and Index failed - WGBS - Bisulfite analysis
BWA
Biscuit
Bisulfite
updated 1 day ago by
Ram
45k • written 1 day ago by
Palanikumar.Palanichamy
• 0
0
votes
3
replies
188
views
illumina: Adapter Confusion
ILLUMINA
ADAPTER
updated 1 day ago by
GenoMax
149k • written 1 day ago by
lingjun meng
▴ 20
2
votes
3
replies
204
views
Identifying primer sequences from raw FASTQ files
primers
20 hours ago by
Chandini
• 0
2
votes
7
replies
1.3k
views
HTSlib threads when ingesting large bgzipped FASTA
htslib
samtools
bgzip
c
updated 1 day ago by
aw7
▴ 370 • written 20 months ago by
Oleksii
• 0
3
votes
3
replies
247
views
question for dowloading Protein fasta sequence by edirect using while
edirect
updated 2 days ago by
vkkodali_ncbi
★ 3.8k • written 2 days ago by
诗友
• 0
2
votes
2
replies
661
views
Validate RNAseq Models in Microarray Data?
microarray
rnaseq
coxlasso
fpkm
updated 1 day ago by
ATpoint
87k • written 2.7 years ago by
vitor
▴ 130
0
votes
0
replies
113
views
Restrict anlaysis of WGS VCF file to Refseq Select using snpeff
refseq
vcf
wgs
2 days ago by
Gabriel
• 0
0
votes
2
replies
199
views
Novel genes in model organisms
homologue
genome
gene
2 days ago by
zizigolu
★ 4.3k
0
votes
1
reply
196
views
Understanding sctransform
sctransform
Seurat
updated 2 days ago by
Bastien Hervé
6.1k • written 2 days ago by
Deepak Tanwar
★ 4.2k
1
vote
1
reply
217
views
Subset reads based on Phred-score ranges
phred
sequencing
ngs
updated 2 days ago by
GenoMax
149k • written 2 days ago by
Mark
▴ 30
5
votes
3
replies
277
views
Reasoning - Why is it invalid to compare ratios of TPMs?
RNAseq
analysis
expression
normalization
differential
TPM
batch
effect
updated 16 hours ago by
ATpoint
87k • written 2 days ago by
VTh
• 0
2
votes
2
replies
332
views
DEGs Analysis For a Microarray Data that has one biological replicates per cell line in each condition
Analysis
DEGs
Microarray
2 days ago by
mete.han.celebi
• 0
2
votes
6
replies
352
views
The soapdenovo2 genome assembly is highly fragmented - learning genome assembly with public data
Gene
soapdenovo2
assembly
updated 2 days ago by
lieven.sterck
15k • written 3 days ago by
JieQY
• 0
0
votes
2
replies
205
views
Cytoscape COLOUR EDGES
Reulatory
Cytoscape
Networks
1 day ago by
SKY
▴ 60
3
votes
3
replies
509
views
VCF filtering with Allele Balance (AB) using FilterVcf (Picard)
Allele-Balance
FilterVcf
Picard
GATK
updated 3 days ago by
GokalpC
▴ 160 • written 15 days ago by
Eduardo
▴ 20
1
vote
4
replies
547
views
Haplotype analysis
founder
haplotype-analysis
1 day ago by
disha3786
• 0
3
votes
4
replies
344
views
Indica rice genome and annotation files
RNASeq
updated 3 days ago by
ChanderKant (CK) Chaudhary
▴ 10 • written 4 days ago by
chandimaa
• 0
2
votes
6
replies
405
views
Question: Making primers for cloning and transfection
transfection
cloning
primer
PCR
gene
updated 2 days ago by
jared.andrews07
★ 18k • written 3 days ago by
Lu Adr
• 0
0
votes
0
replies
163
views
Help with the interpretation of Silhouette width averaging
clustering
kmeans
cluster
silhouettemethod
3 days ago by
Maria Jose
• 0
0
votes
1
reply
233
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Cancer
Oncology
Tenure-earning
Faculty
Bioinformatics
updated 3 days ago by
GenoMax
149k • written 3 days ago by
maritza.garcia-saavedra
• 0
0
votes
1
reply
213
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Oncology
Faculty
Leadership
updated 3 days ago by
GenoMax
149k • written 3 days ago by
maritza.garcia-saavedra
• 0
35
votes
14
replies
1.3k
views
12 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
written 6 weeks ago by
sviatoslav.kendall
▴ 960
0
votes
0
replies
369
views
Tutorial:
CC-By 4.0 Project (unpublished papers and data) release on OSF - Discoveries of 2nd/3rd order gene combinations for static/time series data in cell/…
MachineLearning
SensitivityAnalysis
CellSignaling
GeneCombination
2 hours ago by
sinha.shriprakash
▴ 20
1
vote
1
reply
210
views
Pre-Alignment process
read_depth_measure
updated 3 days ago by
GenoMax
149k • written 3 days ago by
AIMAR
• 0
0
votes
0
replies
175
views
Differential methylation analysis using Dorado
dorado
m6A
DRS
nanopore
3 days ago by
baibhu1234
▴ 20
0
votes
0
replies
163
views
Annotate Phylogentic Tree with classes
python
tree
phylogenetic
analysis
3 days ago by
BIANCA
• 0
120,710 results • Page
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Recent Votes
Answer: merge large amount of fastq files into a single one
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
Answer: Multiple factors in DESeq2
Answer: Multiple factors in DESeq2
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Recent Replies
Comment: Parsing BAM file per cell from Smart-Seq2 dataset
by
GenoMax
149k
Based on your use of UMI's you appear to have smartseq v.3 data. Since this is single cell data I don't know if plain `STAR` is appropria…
Answer: Interactive UMAP for scRNA-seq Data
by
S
• 0
Hi, I found a great package called [ShinyCell][1] which makes interactive UMAP and many other interactive plots. It's super easy to setu…
Comment: Where Is The Experimental Rna Structure Data?
by
Wayne
★ 2.1k
Related 2025 pre-print: ['NucleoSeeker: Precision Filtering of RNA Databases to Curate High-Quality Datasets'](https://www.biorxiv.org/cont…
Comment: GERP Score for variants
by
Begonia_pavonina
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It seems that the link http://mendel.stanford.edu/SidowLab/downloads/gerp/ is dead now. Would anyone know if it is temporary of definitive?…
Comment: Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argu
by
jared.andrews07
★ 18k
Well, the issue is what it says. You're saying your reference data is single cell, but there's only a single cell for each cell type. It ex…
Answer: How to clarify results from an HLA association analysis - Omnibus tests/HATK/oth
by
grover.sandeep
▴ 20
https://pubmed.ncbi.nlm.nih.gov/37495751/ You can reach me. Sandeep Grover
Comment: enrichGo problem
by
Arup Ghosh
3.3k
Can you share some of the gene names from the `genes` vector?
Comment: nanopore variant calling
by
colindaven
7.3k
You'll get massive coverage for just one gene (maybe 2000+ depending on how long you run the minion for), so you could consider multiple ge…
Comment: Reasoning - Why is it invalid to compare ratios of TPMs?
by
ATpoint
87k
I can only speak for myself, but I have never looked at gene ratios, nor do I see its usecase.
Comment: Alignment algorithm for DNA sequencing
by
ATpoint
87k
> some alignment of DNA sequencing This is not an adequate description of what you achieve to do. Please say why common tools, such as the…
Comment: Alignment algorithm for DNA sequencing
by
GenoMax
149k
You can use `bbmap` with the `local=t` option if you need local alignments. `bowtie v.1.x` does ungapped alignments.
Answer: RepeatMasker UCSC track
by
Michael
55k
> These sequences are located in different regions of the genome and they have different lengths. Err, you are talking about repeats here,…
Comment: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair
by
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149k
Only one tool from BBTools package is formally published: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056 BBTool…
Comment: Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argu
by
GenoMax
149k
Please avoid posting screenshots of text data. You can copy/paste and then format the text as `code` using `101010` button in the editor wi…
Comment: Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argu
by
Pumla
• 0
This is the error i have: ![enter image description here][1] and this is my data: ![enter image description here][2] [1]: /medi…
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