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1,000 results • Page
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Forum:
Understanding behaviour of SCTransform in Seurat
Seurat
normalization
scRNASeq
just now by
yura.grabovska
▴ 90
6
votes
4
replies
439
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
14 days ago by
Estevão
▴ 10
0
votes
0
replies
194
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
24 days ago by
yxwucq
• 0
5
votes
2
replies
365
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 4 weeks ago by
Ram
43k • written 4 weeks ago by
Adi
▴ 20
7
votes
7
replies
1.9k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 4 weeks ago by
Dunois
★ 2.5k • written 4 weeks ago by
AdviceSeeker
• 0
1
vote
2
replies
404
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
4 weeks ago by
Javier
• 0
16
votes
10
replies
1.2k
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 6 weeks ago by
Madelaine Gogol
5.3k • written 7 weeks ago by
Ann
★ 2.4k
1
vote
1
reply
244
views
Forum:
Can I use this community for software development?
software-development
updated 7 weeks ago by
Ram
43k • written 7 weeks ago by
avpuzanov
• 0
5
votes
2
replies
407
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 7 weeks ago by
Michael
54k • written 7 weeks ago by
avpuzanov
• 0
0
votes
0
replies
194
views
Forum:
Field of Study in Computational Biology
Genomics
Computational-Biology
PhD
updated 8 weeks ago by
Ram
43k • written 8 weeks ago by
Mohammed
• 0
1
vote
3
replies
510
views
Forum:
Development plan for a bioinformatics database developer/coder
developer
9 weeks ago by
pixie@bioinfo
★ 1.5k
7
votes
8
replies
775
views
Forum:
Bioinformatics career transition
career
forum
updated 9 weeks ago by
jared.andrews07
★ 16k • written 9 weeks ago by
jevill17
▴ 20
4
votes
2
replies
530
views
Forum:
Exploring Amino Acid Patterns in Proteins Through N-gram Analysis
protein
CAFA5
9 weeks ago by
Anatoly A.
▴ 10
6
votes
6
replies
809
views
Forum:
You have 3 days of zero obligations and expansive resources. What are you building?
hypothetical
thought-experiment
10 weeks ago by
jared.andrews07
★ 16k
0
votes
0
replies
194
views
Forum:
What other data types and pipelines you would like to see from the Genomics Data Commons (GDC)
gdc
tcga
genomics-data-commons
updated 10 weeks ago by
Ram
43k • written 10 weeks ago by
Zhenyu Zhang
★ 1.2k
0
votes
2
replies
431
views
Forum:
What's the state of the art in bacterial whole genome alignment?
whole
genome
alignment
mauve
10 weeks ago by
Dave Carlson
★ 1.7k
33
votes
12
replies
1.1k
views
7 follow
Forum:
Nextflow and self-made pipelines opinion
nextflow
pipeline
data-analysis
11 weeks ago by
karlaarz
▴ 110
5
votes
4
replies
605
views
Forum:
Would reaching out to local labs and startups help with my career transition?
career
volunteering
updated 12 weeks ago by
GenoMax
142k • written 12 weeks ago by
Mango
▴ 10
1
vote
2
replies
404
views
Forum:
Exploring Career Reentry: Challenges and opportunities for Women After Maternity and Childcare Breaks
Maternity
Career-Gap
career-reentry
updated 12 weeks ago by
ATpoint
82k • written 12 weeks ago by
ashaneev07
▴ 20
8
votes
7
replies
867
views
6 follow
Forum:
Tower Server configuration for NGS data analysis
NGS
updated 12 weeks ago by
emmanouil.a
▴ 120 • written 3 months ago by
harasharan
• 0
1
vote
0
replies
306
views
Forum:
list of bioinformatics tools in cancer genomics
mutations
CNA
cancer
genomics
LOH
updated 12 weeks ago by
Pierre Lindenbaum
161k • written 12 weeks ago by
Bogdan
★ 1.4k
4
votes
2
replies
405
views
Forum:
bulk seq vs. sc-seq
scATAC-seq
ATAC-seq
scRNAseq
RNAseq
updated 3 months ago by
dsull
★ 6.0k • written 3 months ago by
SebKittelmann
▴ 10
8
votes
6
replies
2.9k
views
Forum:
Demonstrating Exponential Growth In Pre-School
education
written 10.2 years ago by
Asaf
10k
0
votes
0
replies
217
views
Forum:
tutorial for carrier screening analyses?
carrier-screening
updated 3 months ago by
Ram
43k • written 3 months ago by
Akos
▴ 20
2
votes
3
replies
457
views
Forum:
My Project
Project
CLI
MD-Simulations
Molecular-docking
3 months ago by
Ajay A Shettigar
• 0
17
votes
11
replies
1.0k
views
Forum:
How to overcome the imposter syndrome in bioinformatics?
advice
3 months ago by
sil_bioinfo
▴ 40
10
votes
7
replies
2.3k
views
Forum:
How to learn bioinformatics?
learning
updated 3 months ago by
Samuel Lampa
★ 1.3k • written 24 months ago by
sakichwan
▴ 20
26
votes
27
replies
2.2k
views
10 follow
Forum:
Determining computer time required
computer
hpc
time
updated 4 months ago by
dsull
★ 6.0k • written 4 months ago by
Rozita
▴ 40
7
votes
6
replies
772
views
Forum:
where to work as a bioinformatician (NGS/IA)
employment
omics
ia
ngs
updated 4 months ago by
Ram
43k • written 4 months ago by
Petur
▴ 20
21
votes
12
replies
3.6k
views
Forum:
How to Use Biostars Part-3: Formatting Text and Using GitHub Gists
meta
how-to
documentation
4 months ago by
Ram
43k
2
votes
1
reply
462
views
Forum:
Cataloguing available spatial transcriptomics tools, then linking them together into a workflow?
cytassist
transcriptomics
nanostring
xenium
visium
4 months ago by
LauferVA
4.2k
49
votes
20
replies
2.1k
views
10 follow
Forum:
First experiences matter
first-time
tolerance
updated 4 months ago by
Michael Love
★ 2.6k • written 4 months ago by
Mensur Dlakic
★ 27k
4
votes
3
replies
814
views
Forum:
How to get started in bioinformatics
students
updated 4 months ago by
Ram
43k • written 4 months ago by
Soidihane
▴ 10
2
votes
2
replies
604
views
Forum:
Do batches contain biological variations in omics data (RNAseq or scRNAseq)?
combat
single-cell
omics
batch
rnaseq
updated 4 months ago by
Ram
43k • written 4 months ago by
cwwong13
▴ 40
0
votes
2
replies
3.3k
views
Forum:
I’m considering a career transition from software engineering to bioinformatics. Is it a good fit for me?
career
updated 4 months ago by
GenoMax
142k • written 4 months ago by
Mango
▴ 10
5
votes
3
replies
645
views
Forum:
Binning the rare biosphere
metagenomics
soil
assembly
techniques
binning
updated 5 months ago by
Mensur Dlakic
★ 27k • written 5 months ago by
Konstantin
▴ 20
6
votes
2
replies
692
views
Forum:
how to start Bioinformatics?
basics
updated 5 months ago by
Mensur Dlakic
★ 27k • written 5 months ago by
sajibsuvo70
• 0
19
votes
5
replies
1.2k
views
6 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics
snps
survey
papers
4 months ago by
Raony Guimarães
★ 1.4k
4
votes
6
replies
971
views
6 follow
Forum:
Bioinformatics: what do you think of it in the next 20 years?
future
updated 5 months ago by
Ram
43k • written 5 months ago by
Daniel
• 0
1
vote
1
reply
510
views
Forum:
want to work in open source project/project in bioinformatics
project
updated 5 months ago by
Ram
43k • written 5 months ago by
Afeef
• 0
3
votes
5
replies
1.1k
views
Forum:
Current Trends in Bioinformatics
structural-bioinformatics
updated 5 months ago by
Ram
43k • written 6 months ago by
Paulo
• 0
21
votes
11
replies
2.6k
views
6 follow
Forum:
Rust bioinformatics projects ideas
projects
scRNA-seq
RNA-seq
Rust
updated 5 months ago by
Jeremy Leipzig
22k • written 14 months ago by
bompipi95
▴ 150
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
3
votes
2
replies
644
views
Forum:
RNA-Seq data analysis - question
Python
RNA-Seq
R
updated 6 months ago by
fturner
▴ 10 • written 6 months ago by
sil_bioinfo
▴ 40
0
votes
0
replies
389
views
Forum:
How to learn bioinformatics online?
self-education
education
learning
updated 6 months ago by
Ram
43k • written 6 months ago by
Brian Rey | BioLearn
• 0
6
votes
5
replies
2.3k
views
Forum:
Maintaning internal or private installation of Biostar or a similar Q&A site
Biostars
6 months ago by
tshtatland
▴ 190
7
votes
9
replies
1.5k
views
6 follow
Forum:
Mentor for a beginner bioinformatics student
project
mentor
6 months ago by
UT_FAN
▴ 40
0
votes
0
replies
479
views
Forum:
Steps after doublet detection in single cell data
scRNA
doublet
7 months ago by
ishwarvh
• 0
0
votes
0
replies
370
views
Forum:
Automated Checks And QA
retrospective
7 months ago by
Sasha
▴ 840
7
votes
13
replies
1.4k
views
Forum:
How do you validate and verify your pipeline's software updates?
Validation
Verification
Quality-Assurance
updated 6 months ago by
Ram
43k • written 7 months ago by
kieran
▴ 10
1,000 results • Page
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Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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