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119,128 results • Page 1 of 2383
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0
votes
0
replies
4
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Use of gVCF by clinical sequencing labs
gvcf
31 minutes ago by bdolin ▴ 90
0
votes
0
replies
17
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genome annotation and GFF file formation
MetaEuk GFF whole-genome-annotation
updated 1 hour ago by Ram 44k • written 1 hour ago by manaswiniparija3 ▴ 40
0
votes
0
replies
25
views
how to calculate te RSA values of each residue of a protein using DSSP?
RSA proteins
updated 1 hour ago by Ram 44k • written 2 hours ago by raul enrique • 0
819
votes
169
replies
156k
views
110 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 27 days ago by Biostar 3.0k • written 7.9 years ago by Istvan Albert
101k
2
votes
2
replies
160
views
Outlier after DEseq2 in meta-analysis
meta-analysis rna-seq outlier DESeq2
3 hours ago by astefanovic496 ▴ 10
0
votes
0
replies
30
views
Optimizing mutect/sarek for somatic substitution variant calling
mutect2 tumor-normal sarek variant-calling
updated 3 hours ago by Ram 44k • written 3 hours ago by ramiro.barrantes • 0
0
votes
1
reply
69
views
Appropriate minimum gene set size for gene set enrichment analysis
HTSanalyzer gsea FGSEA
updated 3 hours ago by Ram 44k • written 5 hours ago by Bine ▴ 70
0
votes
0
replies
50
views
News: Course - Introduction to the Analysis of Longitudinal Data in Biology
Using R
Longitudinal-Data R Epidemiology Forecasting Gene-Expression
updated 3 hours ago by Ram 44k • written 7 hours ago by carlopecoraro2 ★ 2.6k
0
votes
0
replies
46
views
missing data in ChromHMM
ChromHMM
updated 3 hours ago by Ram 44k • written 7 hours ago by luminea ▴ 10
1
vote
1
reply
76
views
Help on encode accessions
encode
updated 5 hours ago by GenoMax 146k • written 7 hours ago by tsomakiank ▴ 50
1
vote
4
replies
105
views
Choosing the best representative transcript for a gene
transcript
updated 1 hour ago by Ram 44k • written 7 hours ago by Biodee • 0
0
votes
0
replies
45
views
How to handle RNA seq data with unbalanced % rRNA by group?
fastqscreen rRNA DESeq2 RNAseq DGE
7 hours ago by ev97 ▴ 30
0
votes
1
reply
73
views
Seurat Xenium QC
R Xenium spatial Seurat
updated 7 hours ago by Bastien Hervé 5.7k • written 8 hours ago by
yura.grabovska ▴ 530
4
votes
4
replies
150
views
gtf files for various organism in ucsc
gtf
6 hours ago by 1769mkc ★ 1.2k
0
votes
0
replies
62
views
merging of two assemblies from different short-reads techniques
hybrid illumina assembly DNBSEQ
9 hours ago by Andrew Yu • 0
0
votes
3
replies
301
views
Issue with Downloading Genomes from BVBRC
BVBRC genomes
updated 16 hours ago by GenoMax 146k • written 10 weeks ago by ryanmaroun3 • 0
1
vote
3
replies
155
views
PyMOL scripting with GPUs on LSF
pymol hpc pse lsf structure
updated 9 hours ago by GenoMax 146k • written 19 hours ago by noodle ▴ 590
0
votes
2
replies
205
views
Cluster regions based on similar/dissimilar ChIP-seq signal profile across the
whole region and not just overall mean signal.
clustering chip-seq deeptools
updated 20 hours ago by Ming Tommy Tang ★ 4.4k • written 23 hours ago by rls_08
▴ 40
3
votes
4
replies
236
views
What is wrong with my scripts?
R GDC TCGAbiolinks Bioconductor
updated 20 hours ago by Ming Tommy Tang ★ 4.4k • written 1 day ago by nuorain ▴
30
0
votes
3
replies
197
views
cnvpytor run problem
cnvpytor
updated 9 hours ago by yura.grabovska ▴ 530 • written 1 day ago by hamideh ▴ 20
3
votes
6
replies
289
views
PCA for count data
PCA
9 hours ago by QX ▴ 60
3
votes
2
replies
208
views
cnv_facets run problem
R cnv_facets
10 hours ago by hamideh ▴ 20
5
votes
12
replies
321
views
Merge VCF files by chromosome and Across samples
GATK PICARD MergeVcf vcftools
updated 21 hours ago by Pierre Lindenbaum 164k • written 1 day ago by Maverick ▴
10
0
votes
0
replies
74
views
News: Genomic Data Visualisation in R (online course)
Data-Visualisation Genomic-Data R
1 day ago by carlopecoraro2 ★ 2.6k
2
votes
9
replies
275
views
miRNA mapping with bowtie2 gives low alignment %
bowtie2 alignment mirna
20 hours ago by Ant ▴ 30
0
votes
5
replies
208
views
Does mageck-vispr calculate differently than mageck?
mageck mageck-vispr pooled-screen cripsr
updated 2 hours ago by jared.andrews07 ★ 17k • written 1 day ago by Assa
Yeroslaviz ★ 1.9k
0
votes
3
replies
170
views
What does fully overlapping supplementary alignments mean?
Alignment nanopore minimap2
updated 1 day ago by Michael 55k • written 1 day ago by njornet ▴ 20
0
votes
1
reply
126
views
Germline variants in Cancer
Cancer Tumor-normal Germline-variant
updated 1 day ago by Ram 44k • written 1 day ago by prs ▴ 10
0
votes
7
replies
323
views
Unexplainable missing values in single cell Seurat object
cell single seurat missing values
8 hours ago by Gerard ▴ 10
2
votes
2
replies
253
views
why do I get this error while reading single cell RNA seq data in R
scRNA-seq
updated 1 day ago by ATpoint 85k • written 2 days ago by nuorain ▴ 30
0
votes
2
replies
140
views
Converting ICGC ids to TCGA format
cancer tcga icgc
updated 1 day ago by Ram 44k • written 1 day ago by hadas.samuels • 0
0
votes
0
replies
73
views
Comparison of biodiversity between two locations with a known maximum number of
species
shannon ecologie statistics biodiversity
1 day ago by y. • 0
2
votes
4
replies
321
views
Boxplot with adjustment for variable
R boxplot
updated 1 day ago by zx8754 12k • written 4 days ago by Bine ▴ 70
1
vote
0
replies
118
views
What is the right choice of normalization and preprocessing before WGCNA using
RNAseq data in a cohort?
normalization RNA_seq cohort WGCNA
1 day ago by sukeshinik5 ▴ 50
2
votes
5
replies
1.4k
views
VCF file generated by Gridss not recognised by VEP
NGS variant-calling VEP Gridss
updated 1 day ago by Sunnywy0808 • 0 • written 19 months ago by Reda • 0
0
votes
1
reply
308
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants merging precision-recall
updated 1 day ago by GenoMax 146k • written 6 months ago by Luke • 0
1
vote
2
replies
204
views
Reference genome size for genome size estimation.
genome-size
updated 1 day ago by Ram 44k • written 1 day ago by Shakunthala Natarajan • 0
1
vote
2
replies
246
views
Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
Fastq Fastqc scRNA-seq quality-control
1 day ago by Cooper • 0
4
votes
4
replies
361
views
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
DESeq2 logFC FDR DEGs edgeR
9 hours ago by bioinfo1994 ▴ 10
0
votes
3
replies
470
views
batch correction limma package (bead based assay data)
batch-correction
updated 2 days ago by ATpoint 85k • written 6 days ago by MC_J • 0
7
votes
5
replies
2.9k
views
Limma: is it necessary to log-transform the data?
proteomics limma
updated 2 days ago by MC_J • 0 • written 18 months ago by eodmacmd • 0
3
votes
9
replies
605
views
I need help with this R script. Thanks.
R
updated 1 day ago by Ram 44k • written 3 days ago by nuorain ▴ 30
1
vote
2
replies
286
views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina rRNA RNAseq RNA
updated 3 days ago by GenoMax 146k • written 3 days ago by Umberto ▴ 10
2
votes
3
replies
355
views
Using DNA Methylation Data as Input for ChromHMM
ChromHMM methylation DNA
1 day ago by luminea ▴ 10
0
votes
0
replies
180
views
A question with interpreting heatmaps from limma
RNA-seq limma
updated 2 days ago by Ram 44k • written 3 days ago by lhwh1208 • 0
0
votes
1
reply
226
views
STRUCTURE runs failing: core dumping and slurm exit code 10?
slurm linux STRUCTURE
updated 3 days ago by GenoMax 146k • written 3 days ago by katherinedrotos • 0
0
votes
0
replies
183
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics taxonomy mag annotation
3 days ago by LuciaNhu • 0
1
vote
1
reply
234
views
Comparing whole transcriptome under one condition to the transcriptomes under
other conditions
transcriptomics
updated 1 day ago by dthorbur ★ 2.5k • written 4 days ago by Texx • 0
0
votes
0
replies
191
views
News: Machine Learning for Multi-Omics Integration (online course) -January
13-15, 2025
Machine-Learning Big-Data Multi-Omics Data-Integration Deep-Learning
updated 2 days ago by Ram 44k • written 4 days ago by carlopecoraro2 ★ 2.6k
2
votes
1
reply
233
views
How to make DiffBind Run Faster?
DiffBind ATAC-seq
updated 4 days ago by jared.andrews07 ★ 17k • written 4 days ago by B.N. ▴ 10

119,128 results • Page 1 of 2383
Recent Votes
A: Calculating percentage of reads mapped to a reference genome
Answer: What does secondary (and some other fields) mean in flagstat output?
Comment: miRNA mapping with bowtie2 gives low alignment %
Enrichplot - goplot error
Comment: Merge VCF files by chromosome and Across samples
Comment: Merge VCF files by chromosome and Across samples
A: Assessing chIP-seq plotfingerprint IP strength

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Recent Replies
Comment: Choosing the best representative transcript for a gene by Ram 44k
Maybe the later versions have corrected but canonical defaults to the longest,
atleast using snpEff. VEP seems to handle this better. I do …
Comment: validation approach for CNVs by heureuse • 0
Mendelian Precision is an approach i wanted to use but i'm no longer using it.
Comment: Does mageck-vispr calculate differently than mageck? by jared.andrews07
★ 17k
Presumably, but I haven't dug through the source code to verify. OP, can you
post the full logs from your `vispr` call? And the commands yo…
Comment: how to calculate relative solvent accessibility of all human lysine
residues? by raul enrique • 0
can someone explain this step by step please?
Comment: Choosing the best representative transcript for a gene by ATpoint 85k
The canonical is not always the longest transcript. I support the suggestion to
do gene level analysis. Meaning, use something like tximpo…
Comment: Outlier after DEseq2 in meta-analysis by astefanovic496 ▴ 10
Dear i.sudbery, Thank you for your response and valuable input! I had some
additional thoughts. As I am using the ESTIMATE algorithm to …
Comment: Choosing the best representative transcript for a gene by Ram 44k
What Michael said. You have a few options: You can pick the "canonical" =
longest transcript, or you can use something like MANE to pick th…
Answer: Appropriate minimum gene set size for gene set enrichment analysis by
yura.grabovska ▴ 530
This is very much an empirically defined parameter. It would make sense to
benchmark within your data. Luckingly methods built on top of fg…
Comment: Help on encode accessions by GenoMax 146k
Data organization for ENCODE is described on this page:
https://www.encodeproject.org/help/data-organization/
Comment: gtf files for various organism in ucsc by 1769mkc ★ 1.2k
thank you for the insight i would give it a try and update
Comment: Choosing the best representative transcript for a gene by Michael 55k
There is no such thing as the best transcript, there is the possibility to
select the longest transcript per gene from a transcriptome asse…
Comment: gtf files for various organism in ucsc by michael.ante ★ 3.9k
According to the description [here][1]: > refMrna.fa.gz - RefSeq mRNA from the
same species as the genome. This sequence data is updat…
Comment: Seurat Xenium QC by Bastien Hervé 5.7k
You can check some papers using these technologies to see what QC they apply and
would help you make your own for your dataset. The Seurat …
Comment: Unexplainable missing values in single cell Seurat object by Gerard ▴
10
Oh, sorry. I created individual Seurat objects with Read10x (reading filtered
matrixes) and CreateSeuratObject(min.cells = 3, min.features…
Comment: gtf files for various organism in ucsc by 1769mkc ★ 1.2k
refMrna.fa.gz this contains the gtf? file i was expecting .gtf extension i will
look for it.
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