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116,998 results • Page
1 of 2340
Sort: Rank
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Votes
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0
votes
0
replies
8
views
Trimming tool
Trimmer
tool
10 minutes ago by
GeneC
• 0
0
votes
0
replies
7
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
9 minutes ago by
Ezequiel
• 0
0
votes
0
replies
16
views
GG Sankey plot
GO
sankey_plot
gglpot
58 minutes ago by
ijarne
• 0
0
votes
0
replies
26
views
genomic region of transcription factor
search
HOMER
motif
1 hour ago by
qudrat.nii
▴ 10
1
vote
5
replies
205
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 30 minutes ago by
dthorbur
★ 2.0k • written 18 hours ago by
BATMAN
• 0
0
votes
4
replies
103
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
40
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
yura.grabovska
▴ 90
4
votes
7
replies
421
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 5 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
50
views
constructing pangenome through psvcp
psvcp
pangenome
8 hours ago by
analyst
▴ 50
1
vote
9
replies
219
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
1 hour ago by
ashkan
▴ 160
0
votes
1
reply
81
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 7 hours ago by
dthorbur
★ 2.0k • written 8 hours ago by
Umer
▴ 50
0
votes
2
replies
136
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 hours ago by
Zhenyu Zhang
★ 1.2k • written 18 hours ago by
Ngrin
• 0
4
votes
9
replies
378
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
4 hours ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
149
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 10 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
melissachua90
▴ 70
0
votes
0
replies
56
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
11 hours ago by
Varsha
• 0
0
votes
1
reply
168
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 7 hours ago by
GenoMax
142k • written 15 hours ago by
huxiangyulove
• 0
0
votes
0
replies
73
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
18 hours ago by
O.rka
▴ 720
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 18 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
249
views
Merge clusters in Seurat UMAP
seurat
umap
9 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
78
views
Use of ichor CNA
Dog
CNA
genome
23 hours ago by
sainavyav22
• 0
2
votes
2
replies
189
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 21 hours ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
1
vote
0
replies
92
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 19 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
253
views
Details on salmon index
Salmon
updated 4 hours ago by
Rob
6.6k • written 1 day ago by
Lorenzo
• 0
0
votes
0
replies
84
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
1
reply
134
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
1
vote
1
reply
143
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
m90
▴ 30
0
votes
0
replies
83
views
cat-bgen fail
bgenix
updated 1 day ago by
Ram
43k • written 1 day ago by
lambard
• 0
3
votes
4
replies
263
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 2 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Ali
• 0
3
votes
3
replies
180
views
getting exon coordinates
genomics
updated 1 day ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
0
votes
4
replies
258
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 12 hours ago by
Tony
• 0 • written 1 day ago by
vk
▴ 10
1
vote
5
replies
237
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 19 hours ago by
Ram
43k • written 1 day ago by
manuelmourato25
• 0
3
votes
4
replies
344
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
2
votes
11
replies
641
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
10 hours ago by
egascon
• 0
1
vote
1
reply
141
views
API kegg - IndexError: list index out of range
kegg
API
updated 14 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
88
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
1 day ago by
Novogene
▴ 420
0
votes
0
replies
91
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
224
views
Sam file Header problem
Sam
Header
problem
file
updated 10 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
1
vote
4
replies
224
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 19 hours ago by
Ram
43k • written 2 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
552
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 1 day ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
105
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
1
vote
1
reply
154
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 19 hours ago by
Ram
43k • written 1 day ago by
dwpeng
▴ 10
0
votes
1
reply
132
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 13 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
2
votes
3
replies
213
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
177
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 1 hour ago by
andres.firrincieli
3.6k • written 1 day ago by
mavy
▴ 10
1
vote
1
reply
224
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
159
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
149
views
Add line under stat test
stats
R
updated 14 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
1
vote
5
replies
795
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
116,998 results • Page
1 of 2340
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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• 0
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alanh
▴ 170
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6.0k
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Recent Replies
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
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