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108 results • Page
2 of 3
Sort: replies
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Replies
0
votes
3
replies
319
views
samtools version 1.17 having difficulty parsing a filtering command. advice?
samtools
cell
rnaseq
single
updated 4 days ago by
aw7
▴ 340 • written 4 days ago by
RNAseqer
▴ 270
1
vote
3
replies
1.4k
views
R design on 2-way interaction not displaying all options
modeling
design
limma
deseq
edger
updated 5 days ago by
mflab
• 0 • written 4.3 years ago by
fr
▴ 220
0
votes
3
replies
236
views
cnv detection in cow
cow
cnv
updated 11 hours ago by
dthorbur
★ 2.5k • written 3 days ago by
hamideh
▴ 20
0
votes
3
replies
467
views
Calculating TMB for TCGA data
mutations
maftools
TMB
2 days ago by
Jaber
▴ 30
1
vote
3
replies
445
views
TB-PROFILER DELLY ISSUE
DELLY
TB-PROFILER
updated 1 day ago by
Jody Phelan
▴ 10 • written 4 months ago by
Bhawna
• 0
0
votes
2
replies
526
views
Extract directionality from Reactome
pathways
Reactome
biopax
3 days ago by
Nikolas
• 0
4
votes
2
replies
223
views
issue with percent mitochondria from txt file
seurat
6 days ago by
Synat
• 0
3
votes
2
replies
213
views
RNA-seq data compared to qRT-PCR
RNA-seq
updated 6 days ago by
kai
• 0 • written 6 days ago by
SeoG
• 0
0
votes
2
replies
179
views
Unable to link peaks to genes for multiomics data
multiomics
signac
ATACseq
6 days ago by
bgbs
• 0
5
votes
2
replies
258
views
Global Alignment tool
Python
updated 5 days ago by
Joe
21k • written 15 days ago by
Khaled
• 0
0
votes
2
replies
190
views
Help with treetime ancestral MissingDataError
alignment
treetime
multifasta
updated 5 days ago by
Dave Carlson
★ 2.0k • written 5 days ago by
FJCF
• 0
0
votes
2
replies
218
views
Generating multiple species reference for CellRanger
CellRanger
mkref
10X
updated 5 days ago by
GenoMax
147k • written 5 days ago by
nathansuek
▴ 10
1
vote
2
replies
269
views
BSQR in GATK without known variants
GATK
4 days ago by
fuwamozu
• 0
0
votes
2
replies
311
views
Getting an Expression Matrix from GDC Manifest File
RNAseq
4 days ago by
cthangav
▴ 110
3
votes
2
replies
264
views
scATAC-seq (Sinac)
ATACseq
4 days ago by
Synat
• 0
0
votes
2
replies
231
views
number of SNPs per sample in multi-sample VCF file
VCF
bcftools
updated 4 days ago by
dthorbur
★ 2.5k • written 5 days ago by
reza
▴ 300
3
votes
2
replies
286
views
Fastp Trimming for WGS
fastp
fastq
preprocessing
WGS
updated 3 days ago by
GenoMax
147k • written 3 days ago by
o.h3096
• 0
0
votes
2
replies
520
views
Is It Possible to Calculate Microsatellite Instability (MSI) Directly from MAF Files or TCGA Data?
instability
maf
Microsatellite
MSI
3 days ago by
Jaber
▴ 30
1
vote
2
replies
215
views
Using cutadapt for phased primer cleaning
trimming
1 day ago by
1769mkc
★ 1.2k
2
votes
2
replies
290
views
ATACseq Data Insert Size Plot
InsertSize
ATAC-seq
Picard
17 hours ago by
lingjun meng
▴ 20
2
votes
2
replies
244
views
Finding homologous sequences that have crystal structures
proteins
genes
sequences
homologs
blast
updated 9 hours ago by
Dunois
★ 2.8k • written 2 days ago by
Hansen_869
▴ 80
0
votes
2
replies
179
views
Can I use FDR twice for multiple correction in a two-stage study using omics data.
statistical
omics-data
testing
RNA-seq
8 hours ago by
Apprentice
▴ 170
1
vote
2
replies
238
views
Can you help me understand these lines in the completed braker.log
augustus
braker
genome
annotation
4 hours ago by
Vijith
▴ 90
1
vote
2
replies
556
views
best practices for integrating
scRNA-seq
integration
updated 4 hours ago by
yura.grabovska
▴ 670 • written 19 months ago by
Nal23
▴ 10
0
votes
1
reply
335
views
Comparing solubility and hydrophilicity
protein
hydrophilicity
modelling
pymol
solubility
5 days ago by
Hansen_869
▴ 80
0
votes
1
reply
302
views
Biopython installation error
biopython
updated 5 days ago by
Olivia
• 0 • written 17 days ago by
Oliver
• 0
0
votes
1
reply
199
views
Single cell cluster naming
single-cell
updated 5 days ago by
Ram
44k • written 5 days ago by
sc_confusion
• 0
0
votes
1
reply
187
views
downloading protein seqences from STRING database
STRINGdb
proteinseqences
STIRNGAPI
STRING
updated 5 days ago by
GenoMax
147k • written 5 days ago by
m.ciolek
• 0
0
votes
1
reply
191
views
FST Calculation: Resolving -nan Issue in Population Genetics Analysis
NucleotideDiversity
PacBio
mtDNA
updated 5 days ago by
Michael
55k • written 5 days ago by
hashim.rana11
▴ 40
0
votes
1
reply
128
views
CUT&RUN spike in normalization in differential binding analysis (with replicates).
CUTANDRUN
spikein.
differentialBinding
csaw
updated 12 hours ago by
ATpoint
85k • written 1 day ago by
koleilat.karim
• 0
0
votes
1
reply
164
views
Clustal omega on M1 Mac
alignment
clustal-omega
MacOS
updated 5 days ago by
GenoMax
147k • written 6 days ago by
kate-nelis
• 0
3
votes
1
reply
213
views
Identifying gene copy number in genome assembly
CNV
assembly
copy-number
gene
updated 12 hours ago by
lieven.sterck
15k • written 4 days ago by
pedro.rrmb
• 0
0
votes
1
reply
357
views
IGV large deletions
deletion
IGV
updated 5 days ago by
wakaruszka
▴ 30 • written 5 months ago by
Mohammad Amin
• 0
0
votes
1
reply
152
views
Tool:
Introducing SnakeMake.IO – Enhancing Snakemake Workflow Management
snakemake
updated 11 hours ago by
Juke34
8.9k • written 2 days ago by
snakemakeioapp
• 0
1
vote
1
reply
401
views
Requesting Insights on Potential Complex Structural Event Indicated by IGV
Manta
IGV
variant
translocation
structural
updated 6 days ago by
wakaruszka
▴ 30 • written 8 months ago by
pragnapcu
▴ 10
0
votes
1
reply
69
views
Quantification of RNAseq data
Illumina
RNAseq
updated 5 hours ago by
ATpoint
85k • written 5 hours ago by
ahmedsalahtvi
• 0
0
votes
1
reply
164
views
Global alignment of protein sequences all x all to identify similarities between them
Needle
Protein
Global-alignment
EMBOSS
updated 3 days ago by
Ram
44k • written 3 days ago by
Bruna Avelino
▴ 10
0
votes
1
reply
235
views
Canu errors
genome
assembly
Canu
updated 4 days ago by
colindaven
7.0k • written 5 days ago by
joshua.j.wright
▴ 10
0
votes
1
reply
304
views
Computational tools for predicting novel substrates for a class of enzymes
substrate
catalysis
enzyme
updated 3 days ago by
hakimbazol
▴ 20 • written 12 days ago by
yarrowmadrona
▴ 10
0
votes
0
replies
171
views
Job:
Machine Learning Scientist in Multimodal Data Integration
MultiOmics
ML
AI
6 days ago by
Sergio Martínez Cuesta
▴ 230
0
votes
0
replies
165
views
Subtelomeric coordinates for the human CHM13 T2T genome in BED format
marbl
chm13
subtelomeric
t2t
bed
4 days ago by
eusoleroliva
• 0
0
votes
0
replies
116
views
mutated vs wild type DEG analysis using TCGAbiolinkers for COAD data
TCGAbiolinkers
2 days ago by
RUBA
• 0
0
votes
0
replies
118
views
News:
Genome Assembly and Annotation course (online, 17-21 March 2025)
Genome-Annotation
Nanopore
PacBio
Illumina
Genome-Assembly
6 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
47
views
Help in understanding metadata in TCGA skin cancer RangedSummarizedExperiment
metadata
t
TCGA
9 hours ago by
Lexi
• 0
0
votes
0
replies
130
views
bcftools filter appy to sub regions
bcftools
filter
updated 6 days ago by
Pierre Lindenbaum
164k • written 6 days ago by
qwzhang0601
▴ 80
0
votes
0
replies
173
views
How can I create genetic map for impute2 using vcf files containing SNPs?
imputation
vcftools
snps
plink
impute2
5 days ago by
Sakib
• 0
0
votes
0
replies
122
views
EstiAge files
estiage
mutation
6 days ago by
lorena9132
▴ 10
0
votes
0
replies
141
views
News:
Machine learning reveals unexplored gene/protein combinations in cell signalling pathway (OUP publication)
GeneCombination
Rprogramming
CellSignaling
MachineLearning
1 day ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
52
views
Determining Primary, Intermediate, and Mature Mitochondrial Transcripts, and Inferring mtRNA Gene Boundaries
mitogenome
rna-seq
primary_transcripts
pacbio
7 hours ago by
hashim.rana11
▴ 40
1
vote
0
replies
21
views
Tool:
CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
open-source
deep-learning
single-cell
1 hour ago by
Michael
▴ 10
108 results • Page
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Recent Votes
CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
Answer: Can't convert dog ensembl IDs into gene names
Comment: Can you help me understand these lines in the completed braker.log
best practices for integrating
C: disproportinate fastq sizes from bcl2fastq
C: disproportinate fastq sizes from bcl2fastq
NCBI datasets bulk protein fasta download
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Comment: snRNA-seq of the healthy human brain
by
LChart
4.6k
Unless you have a specific concern, you can likely go ahead and proceed with the analysis. You can generate diagnostic plots of where the d…
Comment: snRNA-seq of the healthy human brain
by
JACKY
▴ 170
@lchart I use Scrublet for doublet detection. This plot shows the data after applying Scrublet. Specifically, I removed all cells with a d…
Comment: snRNA-seq of the healthy human brain
by
LChart
4.6k
The typical worry for "expressing too many genes" is that the cell may be a doublet. You are generally better off using an actual doublet f…
Comment: Can't convert dog ensembl IDs into gene names
by
don
• 0
Thank you! Please don't remove the script on Gist! $ python query_ensembl.py --list organism ... canis_lupus_familiaris ..…
Comment: best practices for integrating
by
yura.grabovska
▴ 670
If you're using Seurat v5, the count and data matrices will be kept as separate layers in the object slots by default so you don't need to …
Comment: Can you help me understand these lines in the completed braker.log
by
Vijith
▴ 90
lieven.sterck, thank you for this suggestion. I will definitely update it if I get an answer to this issue.
Comment: Quantification of RNAseq data
by
ATpoint
85k
If your question is whether poor quality RNA can negatively impact {everything}, then yes. The s*** in s***out principle applies to RNA-seq…
Comment: best practices for integrating
by
zak4010
• 0
Did you ever get any advice on this? I have a dataset organized in a similar way
Comment: Ensembl ID to ENTREZ best converter
by
Arup Ghosh
3.2k
The multiVals options default to returning the first occurrence. You can change the option value to `list` to check for the order of mapped…
Comment: snRNA-seq of the healthy human brain
by
JACKY
▴ 170
@atpoint Yes, but generally speaking, for cells that express, for example, 8,000 genes, does this strike you as unusually high based on yo…
Comment: Can I use FDR twice for multiple correction in a two-stage study using omics dat
by
Apprentice
▴ 170
Thank you for your prompt comment. I am sorry in that context, but I am not asking what statistical analysis method should be used for grou…
Comment: How can I plot a step graph in R?
by
GenoMax
147k
Please use `ADD COMMENT/ADD REPLY` when responding to existing posts. `SUBMIT ANSWER` should only be used for a NEW answer to the original …
Comment: insert figure and code in the post of Biostars?
by
ATpoint
85k
Please be precise, what of the solutions here does not work? Where do you get stuck?
Comment: snRNA-seq of the healthy human brain
by
ATpoint
85k
Look at the data and filter outliers from the bulk of cells. Or annotate first by crude celltypes and then do the filters per celltype. The…
Comment: Has anyone tried absence or presence heatmap ? (Or suggestion)
by
KABILAN
▴ 120
Welcome. You can check the ComplexHeatmap manual in `https://github.com/jokergoo/ComplexHeatmap`.
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