Limit : all time
all time today this week this month this year
1,000 results • Page 3 of 20
Sort: Rank
Rank Views Votes Replies
0
votes
0
replies
94
views
Converting rds file to h5ad and saving raw counts as X
R seurat
updated 8 days ago by 11k • written 8 days ago by ▴ 50
0
votes
1
reply
147
views
Seurat: How to get all genes name of a cell ?
seurat
updated 7 days ago by ★ 1.2k • written 8 days ago by ▴ 640
1
vote
0
replies
234
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 7 days ago by 39k • written 8 days ago by • 0
0
votes
0
replies
103
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course RNA-seq pathway
updated 7 days ago by 39k • written 8 days ago by • 0
2
votes
2
replies
119
views
how to use Hemtools bed2vcf?
vcf linux conversion bed
updated 8 days ago by 154k • written 8 days ago by ▴ 10
0
votes
1
reply
151
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 7 days ago by 39k • written 8 days ago by • 0
0
votes
0
replies
85
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase Databases enzymes Restriction
8 days ago by Mahmoud Reda ▴ 10
1
vote
2
replies
207
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
7 days ago by Pegasus ▴ 90
0
votes
0
replies
121
views
Merging multiple PLINK files
plink merging
8 days ago by Nejla • 0
0
votes
0
replies
119
views
References selected by ExomeDepth CNV
CNV ExomeDepth
updated 8 days ago by 129k • written 8 days ago by • 0
0
votes
2
replies
226
views
BCR/TCR analysis using target capture sequencing data
capture ngs TCR BCR
7 days ago by J.F.Jiang ▴ 900
0
votes
2
replies
206
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping Variant-calling masking
updated 8 days ago by 39k • written 9 days ago by ▴ 130
1
vote
3
replies
704
views
Regular Expression for conversion
Linux grep
updated 7 days ago by 21k • written 20 months ago by ▴ 10
0
votes
1
reply
172
views
weird behaviour on bedtools
bedtools RNA-Seq
updated 7 days ago by 39k • written 9 days ago by ▴ 110
0
votes
2
replies
178
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring gsea r
9 days ago by pg45863 • 0
0
votes
1
reply
140
views
ABySS Process Killed
ABySS genome assembly
updated 9 days ago by 129k • written 9 days ago by • 0
0
votes
0
replies
101
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
9 days ago by narges.bioinf • 0
0
votes
3
replies
230
views
Query qbout single cell sequencing
fastq ScRNA
updated 7 days ago by 39k • written 9 days ago by ▴ 20
0
votes
1
reply
189
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle scRNA-seq Seurat
updated 8 days ago by ▴ 950 • written 9 days ago by • 0
0
votes
1
reply
181
views
Why coordinate sort is required in sambamba depths?
sorting coordinate sambamba linux samtools
updated 9 days ago by 154k • written 9 days ago by ▴ 10
0
votes
4
replies
293
views
I need help with a methyl array data analysis
methyl_array DMPs DMRs beta_value r
9 days ago by Ahmad ▴ 10
0
votes
2
replies
252
views
Error in download library file in expression console software
expression microarray console
7 days ago by Mohammad • 0
0
votes
6
replies
342
views
Demultiplexing bam file
demultiplexing bam_file Iontorrent
9 days ago by hasani.iut6 ▴ 60
1
vote
2
replies
267
views
DEgs RNAseq
RNAseq
9 days ago by Juan • 0
0
votes
0
replies
178
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
7 days ago by Vincent Laufer ★ 2.9k
0
votes
1
reply
246
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 9 days ago by ★ 3.0k • written 10 days ago by • 0
1
vote
1
reply
232
views
DownsampleSam
picard DownsampleSam
updated 10 days ago by 154k • written 10 days ago by • 0
0
votes
1
reply
240
views
Error while running Megahit
Megahit
updated 10 days ago by ★ 23k • written 11 days ago by • 0
2
votes
5
replies
418
views
Cutadapt error: too many parameters.
cutadapt parallel bash
8 days ago by DanielEB_fisk ▴ 10
0
votes
0
replies
197
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
11 days ago by dima • 0
1
vote
0
replies
259
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics single-cell RNA DEG
11 days ago by abbas89 ▴ 10
0
votes
1
reply
767
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure pymol protein pdb python
updated 7 days ago by 21k • written 11 days ago by • 0
0
votes
1
reply
304
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2 RNA-seq DGEA
updated 11 days ago by ★ 2.9k • written 11 days ago by ▴ 10
1
vote
2
replies
271
views
Abyss taking a Long time to run
abyss assembly genome fastq
11 days ago by Maliha ▴ 20
0
votes
2
replies
296
views
Import or read Snapgene .dna files into R
R .dna snapgene
11 days ago by eggrandio ▴ 40
4
votes
4
replies
360
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 7 days ago by 21k • written 12 days ago by ▴ 20
0
votes
0
replies
162
views
BEAST Divergence time Analysis
time BEAST BEAUti divergence
12 days ago by ahmadjoyyia ▴ 10
0
votes
0
replies
183
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq deseq2
updated 11 days ago by 39k • written 12 days ago by ▴ 70
1
vote
1
reply
236
views
Variant Annotation
Variant-Annotation VCF R
updated 11 days ago by 39k • written 12 days ago by • 0
0
votes
2
replies
301
views
too many zeros in 16S rRNA amplicon sequencing data
16S rRNA
23 hours ago by zhangdengwei ▴ 190
0
votes
1
reply
208
views
Finding Kinetic Parameters from Western Blot images
image-processing western-blot
updated 11 days ago by 39k • written 12 days ago by • 0
0
votes
0
replies
165
views
Chipseq data peak calling issue
ChIP-seq RNA sequencing
updated 7 days ago by 39k • written 12 days ago by • 0
0
votes
0
replies
146
views
I want to set the null hypothesis for the test of genetic correlation to rg=1.
correlation LDSC genetic
12 days ago by Apprentice ▴ 140
0
votes
2
replies
275
views
About inconsistent cell counts per samples obtained in small nuclear RNAseq data.
Seurat QC Single-Cell
11 days ago by bk11 ▴ 70
0
votes
1
reply
208
views
Identifying Mutation Frequency Changes in MSAs over time?
Mutation Fasta MSA MutationRate RNA-Seq
updated 12 days ago by ★ 2.9k • written 12 days ago by ▴ 20
1
vote
1
reply
173
views
Import Pymol into Python Script
Pymol python
updated 12 days ago by ★ 1.8k • written 12 days ago by • 0
1
vote
1
reply
155
views
making metadata file for differential gene expression analysis
RNAseq
updated 13 days ago by ★ 1.6k • written 13 days ago by ▴ 220
1
vote
2
replies
228
views
Create clustered bar chart in R
R ggplot visualization
12 days ago by Prangan ▴ 20
0
votes
0
replies
113
views
Picard's CollectGcBiasMetrics gc-bias plot- help with interpretation
picard gc-bias wes
13 days ago by bompipi95 ▴ 120
0
votes
2
replies
197
views
Repbase database and transposon sequence
TE TSD TIRs Tpase
12 days ago by manaswiniparija3 ▴ 10
1,000 results • Page 3 of 20
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
Recent Locations • All
Switzerland, just now
France, just now
Santiago de Compostela, Spain, 1 minute ago
United States, 1 minute ago
Germany, 3 minutes ago
Italy, 6 minutes ago
Finland, 6 minutes ago
Recent Awards • All
Scholar to GenoMax 129k
Popular Question to lait ▴ 170
Popular Question to blur ▴ 270
Popular Question to Tawny ▴ 180
Scholar to rpolicastro 12k
Teacher to i.sudbery 17k
Scholar to Joel Wallenius ▴ 130
Recent Replies
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by Zhichao • 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values by ATpoint 72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2 by ATpoint 72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values by ATpoint 72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs by GenoMax 129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Traffic: 2243 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6